<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
- <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
<classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
min-jaba-client.jar
regex.jar
saaj.jar
-spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
-spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
vamsas-client.jar
wsdl4j.jar
xercesImpl.jar
<mapID target="biojson" url="html/features/bioJsonFormat.html" />
<mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
<mapID target="siftsmapping" url="html/features/siftsmapping.html" />
<mapID target="pdbchooser" url="html/features/structurechooser.html" />
<mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
<mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
<mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
+ <mapID target="uniprotfts" url="html/features/uniprotsequencefetcher.html#uniprotfts" />
<mapID target="urllinks" url="html/webServices/urllinks.html" />
<mapID target="linksprefs" url="html/features/preferences.html#links" />
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
- <strong>Searching the PDB Database</strong>
+ <a name="pdbfts"><strong>Searching the PDB Database</strong></a>
</p>
<p>To search the PDB, begin typing in the text box. If the
'autosearch' checkbox is enabled, then the results of your query
</p>
<p>
- <strong>Searching the UniProt Database</strong>
+ <a name="uniprotfts"><strong>Searching the UniProt Database</strong></a>
</p>
<p>To search UniProt, simply begin typing in the text box. If the
'autosearch' check box is enabled, then after a short delay (about
--- /dev/null
+# source: IUPAC codes as per http://www.insdc.org/documents/feature_table.html#7.4.1
+DNA
+R AG
+Y TC
+W AT
+S GC
+M AC
+K GT
+H ATC
+B GTC
+V GAC
+D GAT
+N GATC
--- /dev/null
+-- source: ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt (19th March 2018)
+-- SGC3 name edited slightly so as to fit all on one line
+--**************************************************************************
+-- This is the NCBI genetic code table
+-- Initial base data set from Andrzej Elzanowski while at PIR International
+-- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
+-- Base 1-3 of each codon have been added as comments to facilitate
+-- readability at the suggestion of Peter Rice, EMBL
+-- Later additions by Taxonomy Group staff at NCBI
+--
+-- Version 4.2
+-- Added Karyorelict nuclear genetic code 27
+-- Added Condylostoma nuclear genetic code 28
+-- Added Mesodinium nuclear genetic code 29
+-- Added Peritrich nuclear genetic code 30
+-- Added Blastocrithidia nuclear genetic code 31
+--
+-- Version 4.1
+-- Added Pachysolen tannophilus nuclear genetic code 26
+--
+-- Version 4.0
+-- Updated version to reflect numerous undocumented changes:
+-- Corrected start codons for genetic code 25
+-- Name of new genetic code is Candidate Division SR1 and Gracilibacteria
+-- Added candidate division SR1 nuclear genetic code 25
+-- Added GTG as start codon for genetic code 24
+-- Corrected Pterobranchia Mitochondrial genetic code (24)
+-- Added genetic code 24, Pterobranchia Mitochondrial
+-- Genetic code 11 is now Bacterial, Archaeal and Plant Plastid
+-- Fixed capitalization of mitochondrial in codes 22 and 23
+-- Added GTG, ATA, and TTG as alternative start codons to code 13
+--
+-- Version 3.9
+-- Code 14 differs from code 9 only by translating UAA to Tyr rather than
+-- STOP. A recent study (Telford et al, 2000) has found no evidence that
+-- the codon UAA codes for Tyr in the flatworms, but other opinions exist.
+-- There are very few GenBank records that are translated with code 14,
+-- but a test translation shows that retranslating these records with code
+-- 9 can cause premature terminations. Therefore, GenBank will maintain
+-- code 14 until further information becomes available.
+--
+-- Version 3.8
+-- Added GTG start to Echinoderm mitochondrial code, code 9
+--
+-- Version 3.7
+-- Added code 23 Thraustochytrium mitochondrial code
+-- formerly OGMP code 93
+-- submitted by Gertraude Berger, Ph.D.
+--
+-- Version 3.6
+-- Added code 22 TAG-Leu, TCA-stop
+-- found in mitochondrial DNA of Scenedesmus obliquus
+-- submitted by Gertraude Berger, Ph.D.
+-- Organelle Genome Megasequencing Program, Univ Montreal
+--
+-- Version 3.5
+-- Added code 21, Trematode Mitochondrial
+-- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
+-- Added code 16, Chlorophycean Mitochondrial
+-- (TAG can translated to Leucine instaed to STOP in chlorophyceans
+-- and fungi)
+--
+-- Version 3.4
+-- Added CTG,TTG as allowed alternate start codons in Standard code.
+-- Prats et al. 1989, Hann et al. 1992
+--
+-- Version 3.3 - 10/13/95
+-- Added alternate intiation codon ATC to code 5
+-- based on complete mitochondrial genome of honeybee
+-- Crozier and Crozier (1993)
+--
+-- Version 3.2 - 6/24/95
+-- Code Comments
+-- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
+-- 15 Blepharisma Macro.. code added
+-- 5 Invertebrate Mito.. GTG allowed as alternate initiator
+-- 11 Eubacterial renamed to Bacterial as most alternate starts
+-- have been found in Archea
+--
+--
+-- Version 3.1 - 1995
+-- Updated as per Andrzej Elzanowski at NCBI
+-- Complete documentation in NCBI toolkit documentation
+-- Note: 2 genetic codes have been deleted
+--
+-- Old id Use id - Notes
+--
+-- id 7 id 4 - Kinetoplast code now merged in code id 4
+-- id 8 id 1 - all plant chloroplast differences due to RNA edit
+--
+--*************************************************************************
+
+Genetic-code-table ::= {
+ {
+ name "Standard" ,
+ name "SGC0" ,
+ id 1 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Vertebrate Mitochondrial" ,
+ name "SGC1" ,
+ id 2 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
+ sncbieaa "----------**--------------------MMMM----------**---M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Yeast Mitochondrial" ,
+ name "SGC2" ,
+ id 3 ,
+ ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**----------------------MM----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Mold / Protozoan / Coelenterate Mitochondrial; Mycoplasma; Spiroplasma" ,
+ name "SGC3" ,
+ id 4 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--MM------**-------M------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Invertebrate Mitochondrial" ,
+ name "SGC4" ,
+ id 5 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--------------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
+ name "SGC5" ,
+ id 6 ,
+ ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
+ name "SGC8" ,
+ id 9 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Euplotid Nuclear" ,
+ name "SGC9" ,
+ id 10 ,
+ ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Bacterial, Archaeal and Plant Plastid" ,
+ id 11 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**--*----M------------MMMM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Alternative Yeast Nuclear" ,
+ id 12 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Ascidian Mitochondrial" ,
+ id 13 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**----------------------MM---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ },
+ {
+ name "Alternative Flatworm Mitochondrial" ,
+ id 14 ,
+ ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "-----------*-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Blepharisma Macronuclear" ,
+ id 15 ,
+ ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Chlorophycean Mitochondrial" ,
+ id 16 ,
+ ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Trematode Mitochondrial" ,
+ id 21 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Scenedesmus obliquus Mitochondrial" ,
+ id 22 ,
+ ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "------*---*---*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Thraustochytrium Mitochondrial" ,
+ id 23 ,
+ ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--*-------**--*-----------------M--M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Pterobranchia Mitochondrial" ,
+ id 24 ,
+ ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**-------M---------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Candidate Division SR1 and Gracilibacteria" ,
+ id 25 ,
+ ncbieaa "FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "---M------**-----------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Pachysolen tannophilus Nuclear" ,
+ id 26 ,
+ ncbieaa "FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*----M---------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Karyorelict Nuclear" ,
+ id 27 ,
+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Condylostoma Nuclear" ,
+ id 28 ,
+ ncbieaa "FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**--*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Mesodinium Nuclear" ,
+ id 29 ,
+ ncbieaa "FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Peritrich Nuclear" ,
+ id 30 ,
+ ncbieaa "FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "--------------*--------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ } ,
+ {
+ name "Blastocrithidia Nuclear" ,
+ id 31 ,
+ ncbieaa "FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
+ sncbieaa "----------**-----------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ }
+}
action.new_view = New View
action.close = Close
action.add = Add
-action.save_as_default = Save as default
action.save_as = Save as...
action.save = Save
-action.cancel_fetch = Cancel Fetch
action.change_font = Change Font
action.change_font_tree_panel = Change Font (Tree Panel)
action.colour = Colour
action.view_flanking_regions = Show flanking regions
label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment
label.structures_manager = Structures Manager
-label.nickname = Nickname:
label.url = URL
label.url\: = URL:
label.input_file_url = Enter URL or Input File
label.service_action = Service Action:
label.post_url = POST URL:
label.url_suffix = URL Suffix
-label.sequence_source = Sequence Source
label.per_seq = per Sequence
label.result_vertically_separable = Results are vertically separable
label.amend = Amend
label.channels = Channels
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.select_das_service_from_table = Select a DAS service from the table to read a full description here.</font></html>
label.session_update = Session Update
label.new_vamsas_session = New Vamsas Session
action.load_vamsas_session = Load Vamsas Session...
label.save_colours = Save Colours
label.load_colours_tooltip = Load feature colours and filters from file
label.save_colours_tooltip = Save feature colours and filters to file
-label.fetch_das_features = Fetch DAS Features
label.selected_database_to_fetch_from = Selected {0} database {1} to fetch from {2}
label.database_param = Database: {0}
label.example = Example
label.no_pdb_id_in_file = No PDB Id in File
label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
label.error_parsing_text = Error parsing text
-label.enter_local_das_source = Enter Nickname & URL of Local DAS Source
-label.you_can_only_edit_or_remove_local_das_sources = You can only edit or remove local DAS Sources!
-label.public_das_source = Public DAS source - not editable
label.input_alignment_from_url = Input Alignment From URL
label.input_alignment = Input Alignment
label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
label.error_loading_file = Error loading file
label.problems_opening_file = Encountered problems opening {0}!!
label.file_open_error = File open error
-label.no_das_sources_selected_warn = No das sources were selected.\nPlease select some sources and\ntry again.
-label.no_das_sources_selected_title = No DAS Sources Selected
label.colour_scheme_exists_overwrite = Colour scheme {0} exists.\nContinue saving colour scheme as {1}?"
label.duplicate_scheme_name = Duplicate scheme name
label.jalview_new_questionnaire = There is a new Questionnaire available. Would you like to complete it now ?\n
label.connections = Connections
label.output = Output
label.editing = Editing
-label.das_settings = DAS Settings
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
label.details = Details
label.options = Options
label.parameters = Parameters
-label.available_das_sources = Available DAS Sources
-label.full_details = Full Details
-label.authority = Authority
-label.type = Type
label.proxy_server = Proxy Server
label.file_output = File Output
label.select_input_type = Select input type
label.add_sequences = Add Sequences
label.new_window = New Window
label.split_window = Split Window
-label.refresh_available_sources = Refresh Available Sources
-label.use_registry = Use Registry
-label.add_local_source = Add Local Source
label.set_as_default = Set as Default
label.show_labels = Show labels
action.background_colour = Background Colour...
label.view_and_change_parameters_before_running_calculation = View and change parameters before running calculation
label.view_documentation = View documentation
label.select_return_type = Select return type
-label.translation_of_params = Translation of {0}
+label.translation_of_params = Translation of {0} (Table {1})
label.features_for_params = Features for - {0}
label.annotations_for_params = Annotations for - {0}
label.generating_features_for_params = Generating features for - {0}
label.unable_start_web_service_analysis = Unable to start web service analysis
label.job_couldnt_be_started_check_input = The Job couldn't be started. Please check your input, and the Jalview console for any warning messages.
label.prompt_each_time = Prompt each time
-label.use_source = Use Source
label.couldnt_save_project = Couldn't save project
label.error_whilst_saving_current_state_to = Error whilst saving current state to {0}
label.error_whilst_loading_project_from = Error whilst loading project from {0}
exception.invocation_target_calling_url = InvocationTargetException while calling openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException while calling openURL: {0}
exception.interrupted_launching_browser = InterruptedException while launching browser: {0}
-exception.das_source_doesnt_support_sequence_command = Source {0} does not support the sequence command.
-exception.invalid_das_source = Invalid das source: {0}
exception.ebiembl_retrieval_failed_on = EBI EMBL XML retrieval failed on {0}:{1}
exception.no_pdb_records_for_chain = No PDB Records for {0} chain {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Unexpected exception when handling RNAML translation of PDB data
status.processing = Processing...
status.refreshing_web_service_menus = Refreshing Web Service Menus
status.collecting_job_results = Collecting job results.
-status.fetching_das_sequence_features = Fetching DAS Sequence Features
-status.no_das_sources_active = No DAS Sources Active
-status.das_feature_fetching_cancelled = DAS Feature Fetching Cancelled
-status.das_feature_fetching_complete = DAS Feature Fetching Complete
status.fetching_db_refs = Fetching db refs
status.loading_cached_pdb_entries = Loading Cached PDB Entries
status.searching_for_pdb_structures = Searching for PDB Structures
warn.urls_no_jaba = URLs without any JABA Services
info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)
label.test_server = Test Server?
-info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names?
-label.find_uniprot_accession_ids = Find Uniprot Accession Ids
label.new_sequence_fetcher = New Sequence Fetcher
label.additional_sequence_fetcher = Additional Sequence Fetcher
label.select_database_retrieval_source = Select Database Retrieval Source
warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
label.output_seq_details = Output Sequence Details to list all database references
label.urllinks = Links
-label.default_cache_size = Default Cache Size
action.clear_cached_items = Clear Cached Items
label.togglehidden = Show hidden regions
label.quality_descr = Alignment Quality based on Blosum62 scores
label.keep_all_backup_files = Do not delete old backup files
label.keep_only_this_number_of_backup_files = Keep only this number of most recent backup files
label.autodelete_old_backup_files = Autodelete old backup files:
-label.confirm_delete = Always ask
+label.always_ask = Always ask
label.auto_delete = Automatically delete
label.filename = filename
label.braced_oldest = (oldest)
label.delete = Delete
label.rename = Rename
label.keep = Keep
-label.file_info = (modified {0}, size {1})
\ No newline at end of file
+label.file_info = (modified {0}, size {1})
+label.annotation_name = Annotation Name
+label.annotation_description = Annotation Description
+label.edit_annotation_name_description = Edit Annotation Name/Description
+label.alignment = alignment
+label.pca = PCA
+label.create_image_of = Create {0} image of {1}
+label.click_to_edit = Click to edit, right-click for menu
action.new_view = Nueva vista
action.close = Cerrar
action.add = Añadir
-action.save_as_default = Guardar como por defecto
action.save_as = Guardar como
action.save = Guardar
-action.cancel_fetch = Cancelar búsqueda
action.change_font = Cambiar Fuente
action.change_font_tree_panel = Cambiar fuente (panel del árbol)
action.colour = Color
action.view_flanking_regions = Mostrar flancos
label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento
label.structures_manager = Administrar estructuras
-label.nickname = Sobrenombre:
label.url\: = URL:
label.url = URL
label.input_file_url = Introducir URL en el fichero de entrada
label.service_action = Acción de servicio:
label.post_url = POST URL:
label.url_suffix = URL Sufijo
-label.sequence_source = Fuente de la secuencia
label.per_seq = por secuencia
label.result_vertically_separable = Los resultados son separables verticalmente
label.amend = Modificar
label.channels = Canales
label.channel_title_item_count = {0} ({1})
label.blog_item_published_on_date = {0} {1}
-label.select_das_service_from_table = Seleccionar servicio DAS de la tabla para leer una descripción completa aquí.
label.session_update = Actualizar sesión
label.new_vamsas_session = Nueva sesión Vamsas
action.save_vamsas_session = Guardar Sesión Vamsas
label.save_colours = Guardar colores
label.load_colours_tooltip = Cargar colores y filtros desde fichero
label.save_colours_tooltip = Guardar colores y filtros en fichero
-label.fetch_das_features = Recuperar funciones DAS
label.selected_database_to_fetch_from = Seleccionada {0} Base de datos {1} para buscar de {2}
label.database_param = Base de datos: {0}
label.example = Ejemplo
label.no_pdb_id_in_file = No hay un Id PDB en el fichero
label.couldnt_read_pasted_text = No se pudo leer el texto pegado {0}
label.error_parsing_text = Error analizando el texto
-label.enter_local_das_source = Intruduzca el Nickname & URL de la fuente DAS local
-label.you_can_only_edit_or_remove_local_das_sources = Sólo puedes editar o eliminar fuentes DAS locales!
-label.public_das_source = Fuente pública DAS - no editable
label.input_alignment_from_url = Alineamiento de entrada desde URL
label.input_alignment = Alineamiento de entrada
label.couldnt_import_as_vamsas_session = No se pudo importar {0} como una nueva sesión Vamsas.
label.error_loading_file = Error al cargar el fichero
label.problems_opening_file = Encontrados problemas al abrir el fichero {0}!!
label.file_open_error = Error al abrir el fichero
-label.no_das_sources_selected_warn = No han sido seleccionadas fuentes DAS.\nPor favor, seleccione algunas fuentes y\npruebe de nuevo.
-label.no_das_sources_selected_title = No han sido seleccionadas fuentes DAS
label.colour_scheme_exists_overwrite = El esquema de colores {0} ya existe.\nContinuar guardando el esquema de colores como {1}?
label.duplicate_scheme_name = Duplicar nombre de esquema
label.jalview_new_questionnaire = Hay un nuevo cuestionario disponible. Querr\u00EDa completarlo ahora ?\n
label.connections = Conexiones
label.output = Salida
label.editing = Edición
-label.das_settings = Configuración DAS
label.web_services = Servicios web
label.right_click_to_edit_currently_selected_parameter = Haga clic en el botón derecho para editar el parámetro seleccionado actualmente.
label.let_jmol_manage_structure_colours = Permitir que Jmol gestione la estructuras cromáticas
label.details = Detalles
label.options = Opciones
label.parameters = Paramétros
-label.available_das_sources = Fuentes DAS disponibles
-label.full_details = Detalles completos
-label.authority = Autoridad
-label.type = Tipo
label.proxy_server = Servidor proxy
label.file_output = Fichero de salida
label.select_input_type = Seleccionar el tipo de entrada
label.sort_alignment_new_tree = Alinear el alineamiento con el nuevo árbol
label.add_sequences = Añadir secuencias
label.new_window = Nueva ventana
-label.refresh_available_sources = Refrescar las fuentes disponibles
-label.use_registry = Utilizar el registro
-label.add_local_source = Añadir fuente local
label.set_as_default = Establecer por defecto
label.show_labels = Mostrar etiquetas
label.associate_nodes_with = Asociar nodos con
label.view_and_change_parameters_before_running_calculation = Ver y cambiar los parámetros antes de lanzar el cálculo
label.view_documentation = Ver documentación
label.select_return_type = Seleccionar el tipo de retorno
-label.translation_of_params = Traducción de {0}
+label.translation_of_params = Traducción de {0} (Tabla {1})
label.features_for_params = Características de - {0}
label.annotations_for_params = Anotaciones de - {0}
label.generating_features_for_params = Generando características de - {0}
label.unable_start_web_service_analysis = No es posible iniciar el servicio web de análisis
label.job_couldnt_be_started_check_input = El trabajo no puede arrancarse. Por favor, compruebe los parámetros de entrada y los mensajes de advertencia de la consola de Jalview.
label.prompt_each_time = Preguntar siempre
-label.use_source = Fuente
label.couldnt_save_project = No es posible guardar el proyecto
label.error_whilst_saving_current_state_to = Error mientras se guardaba el estado a {0}
label.error_whilst_loading_project_from = Error cargando el proyecto desde {0}
exception.invocation_target_calling_url = InvocationTargetException mientras se invocaba openURL: {0}
exception.illegal_access_calling_url = IllegalAccessException mientras se invocaba openURL: {0}
exception.interrupted_launching_browser = InterruptedException mientras se lanzaba el navegador: {0}
-exception.das_source_doesnt_support_sequence_command = La fuente {0} no soporta el comando sequence.
-exception.invalid_das_source = Fuente DAS no válida: {0}
exception.ebiembl_retrieval_failed_on = La recuperación de datos EBI EMBL XML ha fallado en {0}:{1}
exception.no_pdb_records_for_chain = No se han encontrado registros {0} para la cadena {1}
exception.unexpected_handling_rnaml_translation_for_pdb = Excepcion inesperada cuando se traducían a RNAML los datos PDB
status.processing = Procesando...
status.refreshing_web_service_menus = Refrescando los menús de servicios web
status.collecting_job_results = Recolectando los resultados de los trabajos.
-status.fetching_das_sequence_features = Recuperando las características DAS de las secuencias
-status.no_das_sources_active = No existe ninguna fuente DAS activa
-status.das_feature_fetching_cancelled = Recuperación de características DAS cancelada
-status.das_feature_fetching_complete = Recuperación de características DAS completada
status.fetching_db_refs = Recuperando db refs
label.font_doesnt_have_letters_defined = La fuente no tiene letras definidas\npor lo que no puede emplease\ncon datos de alineamientos
label.font_too_small = Tamaño de la letra es demasiado pequeña
warn.url_must_contain = La URL de la secuencia debe contener $SEQUENCE_ID$, $DB_ACCESSION$ o un regex
info.validate_jabaws_server = \u00BFValidar el servidor JabaWS?\n(Consulte la consola de salida para obtener los resultados)
label.test_server = ¿Probar servidor?
-info.you_want_jalview_to_find_uniprot_accessions = \u00BFDesea que Jalview encuentre\nUniprot Accession ids para los nombres de secuencias dados?
-label.find_uniprot_accession_ids = Buscar Uniprot Accession Ids
label.new_sequence_fetcher = Añadir recuperador de secuencias
label.additional_sequence_fetcher = Recuperador de secuencia adicional
label.select_database_retrieval_source = Seleccionar fuente de recuperación de bases de datos
warn.name_cannot_be_duplicate = Los nombres URL definidos por el usuario deben ser únicos y no pueden ser ids de MIRIAM
label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
label.urllinks = Enlaces
-label.default_cache_size = Tamaño del caché por defecto
action.clear_cached_items = Borrar elementos en caché
label.quality_descr = Calidad de alineamiento basándose en puntuación Blosum62
label.conservation_descr = Conservación del alineamiento total menos de {0}% huecos
label.keep_all_backup_files = No borrar respaldos antiguas
label.keep_only_this_number_of_backup_files = Mantenga solo este número de respaldos más recientes
label.autodelete_old_backup_files = Borrer automáticamente respaldos antiguos:
-label.confirm_delete = Pregunta siempre
+label.always_ask = Pregunta siempre
label.auto_delete = Borrer automáticamente
label.filename = nombre_de_archivo
label.braced_oldest = (mas antiguo)
label.change_increment_decrement = ¿Cambiar de incremento/decremento?
label.was_previous = era {0}
label.newerdelete_replacement_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado y reemplazarse por un archivo aparentemente más antiguo\n''{1}''\t(modificado {3}, tamaño {5}).
-label.confirm_delete_or_rename = Confirmar borrar ''{0}'', o cambiar el nombre a ''{1}''?
+label.confirm_deletion_or_rename = Confirmar borrar ''{0}'', o cambiar el nombre a ''{1}''?
label.newerdelete_line = El archivo de respaldo\n''{0}''\t(modificado {2}, tamaño {4})\nserá borrado pero es mas nuevo que el archivo de respaldo restante más antiguo\n''{1}''\t(modified {3}, size {5}).
-label.confirm_delete = Confirmar eliminar ''{0}''?
+label.confirm_deletion = Confirmar eliminar ''{0}''?
label.delete = Borrar
label.rename = Cambiar
label.keep = Mantener
-label.file_info = (modificado {0}, tamaño {1})
\ No newline at end of file
+label.file_info = (modificado {0}, tamaño {1})
+label.annotation_name = Nombre de la anotación
+label.annotation_description = Descripción de la anotación
+label.edit_annotation_name_description = Editar el nombre/descripción de la anotación
+label.alignment = alineamiento
+label.pca = ACP
+label.create_image_of = Crear imagen {0} de {1}
+label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú
}
/**
+ * Translates cDNA using the specified code table
*
* @return
*/
- public AlignmentI translateCdna()
+ public AlignmentI translateCdna(GeneticCodeI codeTable)
{
AlignedCodonFrame acf = new AlignedCodonFrame();
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
- seqstring[s], acf, pepseqs);
+ seqstring[s], acf, pepseqs, codeTable);
if (newseq != null)
{
* @param acf
* Definition of global ORF alignment reference frame
* @param proteinSeqs
+ * @param codeTable
* @return sequence ready to be added to alignment.
*/
protected SequenceI translateCodingRegion(SequenceI selection,
String seqstring, AlignedCodonFrame acf,
- List<SequenceI> proteinSeqs)
+ List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
{
List<int[]> skip = new ArrayList<>();
int[] skipint = null;
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
- cdp[2]);
- String aa = ResidueProperties.codonTranslate(new String(codon));
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ String aa = codeTable.translate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
if (aa == null)
*/
package jalview.analysis;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Range;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.util.Comparison;
-import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import com.stevesoft.pat.Regex;
-public class Finder
+/**
+ * Implements the search algorithm for the Find dialog
+ */
+public class Finder implements FinderI
{
- /**
- * Implements the search algorithms for the Find dialog box.
+ /*
+ * matched residue locations
*/
- SearchResultsI searchResults;
+ private SearchResultsI searchResults;
- AlignmentI alignment;
+ /*
+ * sequences matched by id or description
+ */
+ private Vector<SequenceI> idMatches;
- SequenceGroup selection = null;
+ /*
+ * the viewport to search over
+ */
+ private AlignViewportI viewport;
- Vector<SequenceI> idMatch = null;
+ /*
+ * sequence index in alignment to search from
+ */
+ private int sequenceIndex;
- boolean caseSensitive = false;
+ /*
+ * column position in sequence to search from, base 0
+ * - absolute column number including any hidden columns
+ * (position after start of last match for a repeat search)
+ */
+ private int columnIndex;
- private boolean includeDescription = false;
+ /**
+ * Constructor for searching a viewport
+ *
+ * @param av
+ */
+ public Finder(AlignViewportI av)
+ {
+ this.viewport = av;
+ this.sequenceIndex = 0;
+ this.columnIndex = -1;
+ }
- boolean findAll = false;
+ @Override
+ public void findAll(String theSearchString, boolean matchCase,
+ boolean searchDescription)
+ {
+ /*
+ * search from the start
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
- Regex regex = null;
+ doFind(theSearchString, matchCase, searchDescription, true);
- /**
- * holds last-searched position between calls to find(false)
- */
- int seqIndex = 0, resIndex = -1;
+ /*
+ * reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
- public Finder(AlignmentI alignment, SequenceGroup selection)
+ @Override
+ public void findNext(String theSearchString, boolean matchCase,
+ boolean searchDescription)
{
- this.alignment = alignment;
- this.selection = selection;
+ doFind(theSearchString, matchCase, searchDescription, false);
+
+ if (searchResults.isEmpty() && idMatches.isEmpty())
+ {
+ /*
+ * search failed - reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
}
/**
- * restart search at given sequence and residue on alignment and (optionally)
- * contained in selection
+ * Performs a 'find next' or 'find all'
*
- * @param alignment
- * @param selectionGroup
- * @param seqIndex
- * @param resIndex
+ * @param theSearchString
+ * @param matchCase
+ * @param searchDescription
+ * @param findAll
*/
- public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
- int seqIndex, int resIndex)
+ protected void doFind(String theSearchString, boolean matchCase,
+ boolean searchDescription, boolean findAll)
{
- this(alignment, selectionGroup);
- this.seqIndex = seqIndex;
- this.resIndex = resIndex;
- }
+ String searchString = matchCase ? theSearchString
+ : theSearchString.toUpperCase();
+ Regex searchPattern = new Regex(searchString);
+ searchPattern.setIgnoreCase(!matchCase);
- public boolean find(String searchString)
- {
- boolean hasResults = false;
- if (!caseSensitive)
- {
- searchString = searchString.toUpperCase();
- }
- regex = new Regex(searchString);
- regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
- idMatch = new Vector<SequenceI>();
- String item = null;
- boolean found = false;
- int end = alignment.getHeight();
+ idMatches = new Vector<>();
- // /////////////////////////////////////////////
-
- if (selection != null)
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null && selection.getSize() < 1)
{
- if ((selection.getSize() < 1)
- || ((selection.getEndRes() - selection.getStartRes()) < 2))
- {
- selection = null;
- }
+ selection = null; // ? ignore column-only selection
}
- SearchResultMatchI lastm = null;
- while (!found && (seqIndex < end))
- {
- SequenceI seq = alignment.getSequenceAt(seqIndex);
+ AlignmentI alignment = viewport.getAlignment();
+ int end = alignment.getHeight();
- if ((selection != null && selection.getSize() > 0)
- && !selection.getSequences(null).contains(seq))
+ while (sequenceIndex < end)
+ {
+ SequenceI seq = alignment.getSequenceAt(sequenceIndex);
+ boolean found = findNextMatch(seq, searchString, searchPattern,
+ searchDescription);
+ if (found && !findAll)
{
- seqIndex++;
- resIndex = -1;
-
- continue;
+ return;
}
- if (resIndex < 0)
+ if (!found)
{
- resIndex = 0;
- // test for one off matches - sequence position and sequence ID
- // //// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- // possibly a residue number - check if valid for seq
- if (seq.getEnd() >= res)
- {
- searchResults.addResult(seq, res, res);
- hasResults = true;
- // resIndex=seq.getLength();
- // seqIndex++;
- if (!findAll)
- {
- found = true;
- break;
- }
- }
- } catch (NumberFormatException ex)
- {
- }
-
- if (regex.search(seq.getName()) && !idMatch.contains(seq))
- {
- idMatch.addElement(seq);
- hasResults = true;
- if (!findAll)
- {
- // stop and return the match
- found = true;
- break;
- }
- }
-
- if (isIncludeDescription() && seq.getDescription() != null
- && regex.search(seq.getDescription())
- && !idMatch.contains(seq))
- {
- idMatch.addElement(seq);
- hasResults = true;
- if (!findAll)
- {
- // stop and return the match
- found = true;
- break;
- }
- }
+ sequenceIndex++;
+ columnIndex = -1;
}
- item = seq.getSequenceAsString();
+ }
+ }
- if ((selection != null)
- && (selection.getEndRes() < alignment.getWidth() - 1))
- {
- item = item.substring(0, selection.getEndRes() + 1);
- }
+ /**
+ * Answers the start-end column range of the visible region of
+ * <code>sequence</code> starting at or after the given <code>column</code>.
+ * If there are no hidden columns, this just returns the remaining width of
+ * the sequence. The range is restricted to the current <code>selection</code>
+ * if there is one. Answers null if there are no visible columns at or after
+ * <code>column</code>.
+ */
+ protected Range getNextVisibleSequenceRegion(SequenceI sequence,
+ int column)
+ {
+ int seqColStart = column;
+ int seqColEnd = sequence.getLength() - 1;
- // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
- StringBuilder noGapsSB = new StringBuilder();
- int insertCount = 0;
- List<Integer> spaces = new ArrayList<Integer>();
+ /*
+ * restrict search to (next) visible column region,
+ * in case there are hidden columns
+ */
+ AlignmentI alignment = viewport.getAlignment();
+ VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
+ .getVisContigsIterator(column, alignment.getWidth(),
+ false);
+ int[] visible = visibleRegions.hasNext() ? visibleRegions.next() : null;
+ if (visible == null)
+ {
+ columnIndex = seqColEnd + 1;
+ return null;
+ }
+ seqColStart = Math.max(seqColStart, visible[0]);
+ seqColEnd = Math.min(seqColEnd, visible[1]);
- for (int j = 0; j < item.length(); j++)
+ /*
+ * restrict search to selected region if there is one
+ */
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null)
+ {
+ int selectionStart = selection.getStartRes();
+ int selectionEnd = selection.getEndRes();
+ if (selectionStart > seqColEnd || selectionEnd < seqColStart)
{
- if (!Comparison.isGap(item.charAt(j)))
- {
- noGapsSB.append(item.charAt(j));
- spaces.add(Integer.valueOf(insertCount));
- }
- else
- {
- insertCount++;
- }
+ /*
+ * sequence region doesn't overlap selection region
+ */
+ columnIndex = seqColEnd + 1;
+ return null;
}
+ seqColStart = Math.max(seqColStart, selectionStart);
+ seqColEnd = Math.min(seqColEnd, selectionEnd);
+ }
- String noGaps = noGapsSB.toString();
- for (int r = resIndex; r < noGaps.length(); r++)
- {
+ return new Range(seqColStart, seqColEnd);
+ }
- if (regex.searchFrom(noGaps, r))
- {
- resIndex = regex.matchedFrom();
-
- if ((selection != null && selection.getSize() > 0) && (resIndex
- + spaces.get(resIndex) < selection.getStartRes()))
- {
- continue;
- }
- // if invalid string used, then regex has no matched to/from
- int sres = seq.findPosition(resIndex + spaces.get(resIndex));
- int eres = seq.findPosition(regex.matchedTo() - 1
- + (spaces.get(regex.matchedTo() - 1)));
- // only add result if not contained in previous result
- if (lastm == null || (lastm.getSequence() != seq
- || (!(lastm.getStart() <= sres
- && lastm.getEnd() >= eres))))
- {
- lastm = searchResults.addResult(seq, sres, eres);
- }
- hasResults = true;
- if (!findAll)
- {
- // thats enough, break and display the result
- found = true;
- resIndex++;
-
- break;
- }
-
- r = resIndex;
- }
- else
- {
- break;
- }
- }
+ /**
+ * Finds the next match in the given sequence, starting at column at
+ * <code>columnIndex</code>. Answers true if a match is found, else false. If
+ * a match is found, <code>columnIndex</code> is advanced to the column after
+ * the start of the matched region, ready for a search from the next position.
+ *
+ * @param seq
+ * @param searchString
+ * @param searchPattern
+ * @param matchDescription
+ * @return
+ */
+ protected boolean findNextMatch(SequenceI seq, String searchString,
+ Regex searchPattern, boolean matchDescription)
+ {
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null && !selection.contains(seq))
+ {
+ /*
+ * this sequence is not in the selection - advance to next sequence
+ */
+ return false;
+ }
- if (!found)
+ if (columnIndex < 0)
+ {
+ /*
+ * at start of sequence; try find by residue number, in sequence id,
+ * or (optionally) in sequence description
+ */
+ if (doNonMotifSearches(seq, searchString, searchPattern,
+ matchDescription))
{
- seqIndex++;
- resIndex = -1;
+ return true;
}
}
- /**
- * We now search the Id string in the main search loop. for (int id = 0; id
- * < alignment.getHeight(); id++) { if
- * (regex.search(alignment.getSequenceAt(id).getName())) {
- * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
+ /*
+ * search for next match in sequence string
*/
- return hasResults;
- }
-
- /**
- * @return the alignment
- */
- public AlignmentI getAlignment()
- {
- return alignment;
+ int end = seq.getLength();
+ while (columnIndex < end)
+ {
+ if (searchNextVisibleRegion(seq, searchPattern))
+ {
+ return true;
+ }
+ }
+ return false;
}
/**
- * @param alignment
- * the alignment to set
+ * Searches the sequence, starting from <code>columnIndex</code>, and adds the
+ * next match (if any) to <code>searchResults</code>. The search is restricted
+ * to the next visible column region, and to the <code>selection</code> region
+ * if there is one. Answers true if a match is added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public void setAlignment(AlignmentI alignment)
+ protected boolean searchNextVisibleRegion(SequenceI seq, Regex searchPattern)
{
- this.alignment = alignment;
- }
+ Range visible = getNextVisibleSequenceRegion(seq, columnIndex);
+ if (visible == null)
+ {
+ return false;
+ }
+ String seqString = seq.getSequenceAsString(visible.start, visible.end + 1);
+ String noGaps = AlignSeq.extractGaps(Comparison.GapChars, seqString);
- /**
- * @return the caseSensitive
- */
- public boolean isCaseSensitive()
- {
- return caseSensitive;
- }
+ if (searchPattern.search(noGaps))
+ {
+ int sequenceStartPosition = seq.findPosition(visible.start);
+ recordMatch(seq, searchPattern, sequenceStartPosition);
+ return true;
+ }
+ else
+ {
+ /*
+ * no match - advance columnIndex past this visible region
+ * so the next visible region (if any) is searched next
+ */
+ columnIndex = visible.end + 1;
+ }
- /**
- * @param caseSensitive
- * the caseSensitive to set
- */
- public void setCaseSensitive(boolean caseSensitive)
- {
- this.caseSensitive = caseSensitive;
+ return false;
}
/**
- * @return the findAll
+ * Adds the match held in the <code>searchPattern</code> Regex to the
+ * <code>searchResults</code>, unless it is a subregion of the last match
+ * recorded. <code>columnIndex</code> is advanced to the position after the
+ * start of the matched region, ready for the next search. Answers true if a
+ * match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @param firstResiduePosition
+ * @return
*/
- public boolean isFindAll()
+ protected boolean recordMatch(SequenceI seq, Regex searchPattern,
+ int firstResiduePosition)
{
- return findAll;
- }
+ /*
+ * get start/end of the match in sequence coordinates
+ */
+ int offset = searchPattern.matchedFrom();
+ int matchStartPosition = firstResiduePosition + offset;
+ int matchEndPosition = matchStartPosition
+ + searchPattern.charsMatched() - 1;
+
+ /*
+ * update columnIndex to next column after the start of the match
+ * (findIndex returns a value base 1, columnIndex is held base 0)
+ */
+ columnIndex = seq.findIndex(matchStartPosition);
- /**
- * @param findAll
- * the findAll to set
- */
- public void setFindAll(boolean findAll)
- {
- this.findAll = findAll;
- }
+ /*
+ * check that this match is not a subset of the previous one (JAL-2302)
+ */
+ List<SearchResultMatchI> matches = searchResults.getResults();
+ SearchResultMatchI lastMatch = matches.isEmpty() ? null
+ : matches.get(matches.size() - 1);
- /**
- * @return the selection
- */
- public jalview.datamodel.SequenceGroup getSelection()
- {
- return selection;
- }
+ if (lastMatch == null || !lastMatch.contains(seq, matchStartPosition,
+ matchEndPosition))
+ {
+ searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+ return true;
+ }
- /**
- * @param selection
- * the selection to set
- */
- public void setSelection(jalview.datamodel.SequenceGroup selection)
- {
- this.selection = selection;
+ return false;
}
/**
- * Returns the (possibly empty) list of matching sequences (when search
- * includes searching sequence names)
+ * Does searches other than for residue patterns. Currently this includes
+ * <ul>
+ * <li>find residue by position (if search string is a number)</li>
+ * <li>match search string to sequence id</li>
+ * <li>match search string to sequence description (optional)</li>
+ * </ul>
+ * Answers true if a match is found, else false.
*
+ * @param seq
+ * @param searchString
+ * @param searchPattern
+ * @param includeDescription
* @return
*/
- public Vector<SequenceI> getIdMatch()
+ protected boolean doNonMotifSearches(SequenceI seq, String searchString,
+ Regex searchPattern, boolean includeDescription)
{
- return idMatch;
- }
+ /*
+ * position sequence search to start of sequence
+ */
+ columnIndex = 0;
- /**
- * @return the regex
- */
- public com.stevesoft.pat.Regex getRegex()
- {
- return regex;
+ if (searchForResidueNumber(seq, searchString))
+ {
+ return true;
+ }
+ if (searchSequenceName(seq, searchPattern))
+ {
+ return true;
+ }
+ if (includeDescription && searchSequenceDescription(seq, searchPattern))
+ {
+ return true;
+ }
+ return false;
}
/**
- * @return the searchResults
+ * Searches for a match with the sequence description, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public SearchResultsI getSearchResults()
+ protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
{
- return searchResults;
+ String desc = seq.getDescription();
+ if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(seq);
+ return true;
+ }
+ return false;
}
/**
- * @return the resIndex
+ * Searches for a match with the sequence name, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
*/
- public int getResIndex()
+ protected boolean searchSequenceName(SequenceI seq, Regex searchPattern)
{
- return resIndex;
+ if (searchPattern.search(seq.getName()) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(seq);
+ return true;
+ }
+ return false;
}
/**
- * @param resIndex
- * the resIndex to set
+ * Tries to interpret the search string as a residue position, and if valid,
+ * adds the position to the search results and returns true, else answers
+ * false
*/
- public void setResIndex(int resIndex)
+ protected boolean searchForResidueNumber(SequenceI seq, String searchString)
{
- this.resIndex = resIndex;
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ if (seq.getStart() <= res && seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ return true;
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+ return false;
}
- /**
- * @return the seqIndex
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getIdMatch()
*/
- public int getSeqIndex()
+ @Override
+ public Vector<SequenceI> getIdMatches()
{
- return seqIndex;
+ return idMatches;
}
- /**
- * @param seqIndex
- * the seqIndex to set
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getSearchResults()
*/
- public void setSeqIndex(int seqIndex)
- {
- this.seqIndex = seqIndex;
- }
-
- public boolean isIncludeDescription()
- {
- return includeDescription;
- }
-
- public void setIncludeDescription(boolean includeDescription)
+ @Override
+ public SearchResultsI getSearchResults()
{
- this.includeDescription = includeDescription;
+ return searchResults;
}
}
--- /dev/null
+package jalview.analysis;
+
+public interface GeneticCodeI
+{
+ /**
+ * Answers the single letter amino acid code (e.g. "D") for the given codon
+ * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
+ * codon is not case-sensitive, the return value is upper case.
+ * <p>
+ * If the codon includes any of the standard ambiguity codes
+ * <ul>
+ * <li>if all possible translations are the same, returns that value</li>
+ * <li>else returns null</li>
+ * </ul>
+ *
+ * @param codon
+ * @return
+ */
+ String translate(String codon);
+
+ /**
+ * Answers the single letter amino acid code (e.g. "D") for the given codon
+ * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
+ * codon is not case-sensitive, the return value is upper case. If the codon
+ * includes any of the standard ambiguity codes, this method returns null.
+ *
+ * @param codon
+ * @return
+ */
+ String translateCanonical(String codon);
+
+ /**
+ * Answers a unique identifier for the genetic code (using the numbering
+ * system as on NCBI)
+ *
+ * @return
+ */
+ String getId();
+
+ /**
+ * Answers a display name suitable for use in menus, reports etc
+ *
+ * @return
+ */
+ String getName();
+}
--- /dev/null
+package jalview.analysis;
+
+import jalview.bin.Cache;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+/**
+ * A singleton that provides instances of genetic code translation tables
+ *
+ * @author gmcarstairs
+ * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
+ */
+public final class GeneticCodes
+{
+ private static final int CODON_LENGTH = 3;
+
+ private static final String QUOTE = "\"";
+
+ /*
+ * nucleotides as ordered in data file
+ */
+ private static final String NUCS = "TCAG";
+
+ private static final int NUCS_COUNT = NUCS.length();
+
+ private static final int NUCS_COUNT_SQUARED = NUCS_COUNT * NUCS_COUNT;
+
+ private static final int NUCS_COUNT_CUBED = NUCS_COUNT * NUCS_COUNT
+ * NUCS_COUNT;
+
+ private static final String AMBIGUITY_CODES_FILE = "/AmbiguityCodes.dat";
+
+ private static final String RESOURCE_FILE = "/GeneticCodes.dat";
+
+ private static GeneticCodes instance = new GeneticCodes();
+
+ private Map<String, String> ambiguityCodes;
+
+ /*
+ * loaded code tables, with keys in order of loading
+ */
+ private Map<String, GeneticCodeI> codeTables;
+
+ /**
+ * Private constructor enforces singleton
+ */
+ private GeneticCodes()
+ {
+ if (instance == null)
+ {
+ ambiguityCodes = new HashMap<>();
+
+ /*
+ * LinkedHashMap preserves order of addition of entries,
+ * so we can assume the Standard Code Table is the first
+ */
+ codeTables = new LinkedHashMap<>();
+ loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
+ loadCodes(RESOURCE_FILE);
+ }
+ };
+
+ /**
+ * Returns the singleton instance of this class
+ *
+ * @return
+ */
+ public static GeneticCodes getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * Returns the known code tables, in order of loading.
+ *
+ * @return
+ */
+ public Iterable<GeneticCodeI> getCodeTables()
+ {
+ return codeTables.values();
+ }
+
+ /**
+ * Answers the code table with the given id
+ *
+ * @param id
+ * @return
+ */
+ public GeneticCodeI getCodeTable(String id)
+ {
+ return codeTables.get(id);
+ }
+
+ /**
+ * A convenience method that returns the standard code table (table 1). As
+ * implemented, this has to be the first table defined in the data file.
+ *
+ * @return
+ */
+ public GeneticCodeI getStandardCodeTable()
+ {
+ return codeTables.values().iterator().next();
+ }
+
+ /**
+ * Loads the code tables from a data file
+ */
+ protected void loadCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+
+ /*
+ * skip comments and start of table
+ */
+ String line = "";
+ while (line != null && !line.startsWith("Genetic-code-table"))
+ {
+ line = readLine(dataIn);
+ }
+ line = readLine(dataIn);
+
+ while (line.startsWith("{"))
+ {
+ line = loadOneTable(dataIn);
+ }
+ } catch (IOException | NullPointerException e)
+ {
+ Cache.log.error(
+ "Error reading genetic codes data file: "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Reads and saves Nucleotide ambiguity codes from a data file. The file may
+ * include comment lines (starting with #), a header 'DNA', and one line per
+ * ambiguity code, for example:
+ * <p>
+ * R<tab>AG
+ * <p>
+ * means that R is an ambiguity code meaning "A or G"
+ *
+ * @param fileName
+ */
+ protected void loadAmbiguityCodes(String fileName)
+ {
+ try
+ {
+ InputStream is = getClass().getResourceAsStream(fileName);
+ BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
+ String line = "";
+ while (line != null)
+ {
+ line = readLine(dataIn);
+ if (line != null && !"DNA".equals(line.toUpperCase()))
+ {
+ String[] tokens = line.split("\\t");
+ ambiguityCodes.put(tokens[0].toUpperCase(),
+ tokens[1].toUpperCase());
+ }
+ }
+ } catch (IOException e)
+ {
+ Cache.log.error(
+ "Error reading nucleotide ambiguity codes data file: "
+ + e.getMessage());
+ }
+ }
+
+ /**
+ * Reads up to and returns the next non-comment line, trimmed. Comment lines
+ * start with a #. Returns null at end of file.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String readLine(BufferedReader dataIn) throws IOException
+ {
+ String line = dataIn.readLine();
+ while (line != null && line.startsWith("#"))
+ {
+ line = readLine(dataIn);
+ }
+ return line == null ? null : line.trim();
+ }
+
+ /**
+ * Reads the lines of the data file describing one translation table, and
+ * creates and stores an instance of GeneticCodeI. Returns the '{' line
+ * starting the next table, or the '}' line at end of all tables. Data format
+ * is
+ *
+ * <pre>
+ * {
+ * name "Vertebrate Mitochondrial" ,
+ * name "SGC1" ,
+ * id 2 ,
+ * ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
+ * sncbieaa "----------**--------------------MMMM----------**---M------------"
+ * -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ * -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ * -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+ * },
+ * </pre>
+ *
+ * of which we parse the first name, the id, and the ncbieaa translations for
+ * codons as ordered by the Base1/2/3 lines. Note Base1/2/3 are included for
+ * readability and are in a fixed order, these are not parsed. The sncbieaa
+ * line marks alternative start codons, these are not parsed.
+ *
+ * @param dataIn
+ * @return
+ * @throws IOException
+ */
+ protected String loadOneTable(BufferedReader dataIn) throws IOException
+ {
+ String name = null;
+ String id = null;
+ Map<String, String> codons = new HashMap<>();
+
+ String line = readLine(dataIn);
+
+ while (line != null && !line.startsWith("}"))
+ {
+ if (line.startsWith("name") && name == null)
+ {
+ name = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ }
+ else if (line.startsWith("id"))
+ {
+ id = new StringTokenizer(line.substring(2)).nextToken();
+ }
+ else if (line.startsWith("ncbieaa"))
+ {
+ String aminos = line.substring(line.indexOf(QUOTE) + 1,
+ line.lastIndexOf(QUOTE));
+ if (aminos.length() != NUCS_COUNT_CUBED) // 4 * 4 * 4 combinations
+ {
+ Cache.log.error("wrong data length in code table: " + line);
+ }
+ else
+ {
+ for (int i = 0; i < aminos.length(); i++)
+ {
+ String peptide = String.valueOf(aminos.charAt(i));
+ char codon1 = NUCS.charAt(i / NUCS_COUNT_SQUARED);
+ char codon2 = NUCS
+ .charAt((i % NUCS_COUNT_SQUARED) / NUCS_COUNT);
+ char codon3 = NUCS.charAt(i % NUCS_COUNT);
+ String codon = new String(
+ new char[]
+ { codon1, codon2, codon3 });
+ codons.put(codon, peptide);
+ }
+ }
+ }
+ line = readLine(dataIn);
+ }
+
+ registerCodeTable(id, name, codons);
+ return readLine(dataIn);
+ }
+
+ /**
+ * Constructs and registers a GeneticCodeI instance with the codon
+ * translations as defined in the data file. For all instances except the
+ * first, any undeclared translations default to those in the standard code
+ * table.
+ *
+ * @param id
+ * @param name
+ * @param codons
+ */
+ protected void registerCodeTable(final String id, final String name,
+ final Map<String, String> codons)
+ {
+ codeTables.put(id, new GeneticCodeI()
+ {
+ /*
+ * map of ambiguous codons to their 'product'
+ * (null if not all possible translations match)
+ */
+ Map<String, String> ambiguous = new HashMap<>();
+
+ @Override
+ public String translateCanonical(String codon)
+ {
+ return codons.get(codon.toUpperCase());
+ }
+
+ @Override
+ public String translate(String codon)
+ {
+ String upper = codon.toUpperCase();
+ String peptide = translateCanonical(upper);
+
+ /*
+ * if still not translated, check for ambiguity codes
+ */
+ if (peptide == null)
+ {
+ peptide = getAmbiguousTranslation(upper, ambiguous, this);
+ }
+ return peptide;
+ }
+
+ @Override
+ public String getId()
+ {
+ return id;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+ });
+ }
+
+ /**
+ * Computes all possible translations of a codon including one or more
+ * ambiguity codes, and stores and returns the result (null if not all
+ * translations match). If the codon includes no ambiguity codes, simply
+ * returns null.
+ *
+ * @param codon
+ * @param ambiguous
+ * @param codeTable
+ * @return
+ */
+ protected String getAmbiguousTranslation(String codon,
+ Map<String, String> ambiguous, GeneticCodeI codeTable)
+ {
+ if (codon.length() != CODON_LENGTH)
+ {
+ return null;
+ }
+
+ boolean isAmbiguous = false;
+
+ char[][] expanded = new char[CODON_LENGTH][];
+ for (int i = 0; i < CODON_LENGTH; i++)
+ {
+ String base = String.valueOf(codon.charAt(i));
+ if (ambiguityCodes.containsKey(base))
+ {
+ isAmbiguous = true;
+ base = ambiguityCodes.get(base);
+ }
+ expanded[i] = base.toCharArray();
+ }
+
+ if (!isAmbiguous)
+ {
+ // no ambiguity code involved here
+ return null;
+ }
+
+ /*
+ * generate and translate all permutations of the ambiguous codon
+ * only return the translation if they all agree, else null
+ */
+ String peptide = null;
+ for (char c1 : expanded[0])
+ {
+ for (char c2 : expanded[1])
+ {
+ for (char c3 : expanded[2])
+ {
+ char[] cdn = new char[] { c1, c2, c3 };
+ String possibleCodon = String.valueOf(cdn);
+ String pep = codeTable.translate(possibleCodon);
+ if (pep == null || (peptide != null && !pep.equals(peptide)))
+ {
+ ambiguous.put(codon, null);
+ return null;
+ }
+ peptide = pep;
+ }
+ }
+ }
+
+ /*
+ * all translations of ambiguous codons matched!
+ */
+ ambiguous.put(codon, peptide);
+ return peptide;
+ }
+}
* @return
*/
boolean isOutwithThreshold(SequenceFeature sf);
+
+ /*
+ * Answers a human-readable text description of the colour, suitable for
+ * display as a tooltip, possibly internationalised for the user's locale.
+ *
+ * @return
+ */
+ String getDescription();
}
--- /dev/null
+package jalview.api;
+
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+/**
+ * An interface for searching for a pattern in an aligment
+ */
+public interface FinderI
+{
+
+ /**
+ * Performs a find for the given search string (interpreted as a regular
+ * expression). Search may optionally be case-sensitive, and may optionally
+ * including match in sequence description (sequence id is always searched).
+ * If the viewport has an active selection, then the find is restricted to the
+ * selection region. Sequences matched by id or description can be retrieved
+ * by getIdMatches(), and matched residue patterns by getSearchResults().
+ *
+ * @param theSearchString
+ * @param caseSensitive
+ * @param searchDescription
+ * @return
+ */
+ void findAll(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
+
+ /**
+ * Finds the next match for the given search string (interpreted as a regular
+ * expression), starting from the position after the last match found. Search
+ * may optionally be case-sensitive, and may optionally including match in
+ * sequence description (sequence id is always searched). If the viewport has
+ * an active selection, then the find is restricted to the selection region.
+ * Sequences matched by id or description can be retrieved by getIdMatches(),
+ * and matched residue patterns by getSearchResults().
+ *
+ * @param theSearchString
+ * @param caseSensitive
+ * @param searchDescription
+ * @return
+ */
+ void findNext(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
+
+ /**
+ * Returns the (possibly empty) list of sequences matched on sequence name or
+ * description
+ *
+ * @return
+ */
+ List<SequenceI> getIdMatches();
+
+ /**
+ * Answers the search results (possibly empty) from the last search
+ *
+ * @return
+ */
+ SearchResultsI getSearchResults();
+
+}
\ No newline at end of file
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(width);
- }
if (x < 0)
{
x = 0;
if (oldcs.isGraduatedColour())
{
threshline.value = oldcs.getThreshold();
- cs = new FeatureColour((FeatureColour) oldcs, min, max);
+ cs = new FeatureColour(oldcs.getColour(), oldcs.getMinColour(),
+ oldcs.getMaxColour(), oldcs.getNoColour(), min, max);
}
else
{
bl = oldcs.getColour();
}
// original colour becomes the maximum colour
- cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(bl, Color.white, bl, Color.white, mm[0],
+ mm[1]);
}
minColour.setBackground(cs.getMinColour());
maxColour.setBackground(cs.getMaxColour());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- FeatureColour acg = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), min, max);
+ Color minc = minColour.getBackground();
+ Color maxc = maxColour.getBackground();
+ FeatureColour acg = new FeatureColour(maxc, minc, maxc, minc, min, max);
acg.setColourByLabel(colourFromLabel.getState());
maxColour.setEnabled(!colourFromLabel.getState());
{
if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- acg = new FeatureColour(acg, threshline.value, max);
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), threshline.value,
+ max);
}
else
{
- acg = new FeatureColour(acg, min, threshline.value);
+ acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
+ acg.getMaxColour(), acg.getNoColour(), min,
+ threshline.value);
}
}
*/
package jalview.appletgui;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
import java.awt.Button;
import java.awt.Checkbox;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
+import java.util.Map;
public class Finder extends Panel implements ActionListener
{
- AlignmentViewport av;
+ private AlignViewportI av;
- AlignmentPanel ap;
+ private AlignmentPanel ap;
- Frame frame;
+ private TextField textfield = new TextField();
- SearchResultsI searchResults;
+ private Button findAll = new Button();
- int seqIndex = 0;
+ private Button findNext = new Button();
- int resIndex = -1;
+ private Button createFeatures = new Button();
+
+ private Checkbox caseSensitive = new Checkbox();
+
+ private Checkbox searchDescription = new Checkbox();
+
+ private SearchResultsI searchResults;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ Map<AlignViewportI, FinderI> finders;
public Finder(final AlignmentPanel ap)
{
+ finders = new HashMap<>();
+
try
{
jbInit();
this.av = ap.av;
this.ap = ap;
- frame = new Frame();
+ Frame frame = new Frame();
frame.add(this);
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("action.find"), 340, 120);
else if (evt.getSource() == findAll)
{
- resIndex = -1;
- seqIndex = 0;
doSearch(true);
}
- else if (evt.getSource() == createNewGroup)
+ else if (evt.getSource() == createFeatures)
{
- createNewGroup_actionPerformed();
+ createFeatures_actionPerformed();
}
}
- public void createNewGroup_actionPerformed()
+ public void createFeatures_actionPerformed()
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
String searchString = textfield.getText().trim();
for (SearchResultMatchI match : searchResults.getResults())
}
}
- void doSearch(boolean findAll)
+ void doSearch(boolean doFindAll)
{
if (ap.av.applet.currentAlignFrame != null)
{
ap = ap.av.applet.currentAlignFrame.alignPanel;
av = ap.av;
}
- createNewGroup.setEnabled(false);
- jalview.analysis.Finder finder = new jalview.analysis.Finder(
- av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.getState());
- finder.setIncludeDescription(searchDescription.getState());
- finder.setFindAll(findAll);
+ createFeatures.setEnabled(false);
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
String searchString = textfield.getText();
-
- finder.find(searchString);
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
- searchResults = finder.getSearchResults();
- Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.getState();
+ boolean doSearchDescription = searchDescription.getState();
+ if (doFindAll)
{
- haveResults = true;
- ap.idPanel.highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
- ap.idPanel.highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
- if (searchResults.getSize() > 0)
- {
- haveResults = true;
- createNewGroup.setEnabled(true);
+ searchResults = finder.getSearchResults();
+
+ List<SequenceI> idMatches = finder.getIdMatches();
+ ap.idPanel.highlightSearchResults(idMatches);
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
// if allResults is null, this effectively switches displaySearch flag in
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatches.isEmpty() && searchResults == null)
{
ap.alignFrame.statusBar.setText(
MessageManager.getString("label.finished_searching"));
- resIndex = -1;
- seqIndex = 0;
}
else
{
- if (findAll)
+ if (doFindAll)
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
: "";
- if (idMatch.size() > 0 && searchResults != null
+ if (idMatches.size() > 0 && searchResults != null
&& searchResults.getSize() > 0)
{
message += " and ";
}
}
- Label jLabel1 = new Label();
-
- protected TextField textfield = new TextField();
-
- protected Button findAll = new Button();
-
- protected Button findNext = new Button();
-
- Panel actionsPanel = new Panel();
-
- GridLayout gridLayout1 = new GridLayout();
-
- protected Button createNewGroup = new Button();
-
- Checkbox caseSensitive = new Checkbox();
-
- Checkbox searchDescription = new Checkbox();
-
private void jbInit() throws Exception
{
+ Label jLabel1 = new Label(MessageManager.getString("action.find"));
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText(MessageManager.getString("action.find"));
jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
this.setLayout(null);
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
@Override
public void keyTyped(KeyEvent e)
{
- textfield_keyTyped(e);
+ textfield_keyTyped();
}
});
textfield.addActionListener(this);
findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
findNext.setLabel(MessageManager.getString("action.find_next"));
findNext.addActionListener(this);
+
+ Panel actionsPanel = new Panel();
actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+ GridLayout gridLayout1 = new GridLayout();
actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
- createNewGroup.setEnabled(false);
- createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
- createNewGroup.addActionListener(this);
+ createFeatures.setEnabled(false);
+ createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ createFeatures.setLabel(MessageManager.getString("label.new_feature"));
+ createFeatures.addActionListener(this);
caseSensitive.setLabel(MessageManager.getString("label.match_case"));
caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
actionsPanel.add(findNext, null);
actionsPanel.add(findAll, null);
- actionsPanel.add(createNewGroup, null);
+ actionsPanel.add(createFeatures, null);
this.add(caseSensitive);
this.add(textfield, null);
this.add(jLabel1, null);
this.add(searchDescription);
}
- void textfield_keyTyped(KeyEvent e)
+ void textfield_keyTyped()
{
findNext.setEnabled(true);
}
protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,
boolean hiddenRows)
{
- int maxwidth = av.getAlignment().getWidth();
+ int maxwidth = av.getAlignment().getVisibleWidth();
int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
-
int annotationHeight = 0;
AnnotationLabels labels = null;
{
idCanvas.setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
{
if (od.isPositionInBox(evt.getX(), evt.getY()))
{
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ this.getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ this.getParent()
+ .setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
+ getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
.visibleToAbsoluteColumn(endx);
}
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
-
// WEST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
int endx;
int ypos = hgap;
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
int blockEnd;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+ VisibleContigsIterator regions = hidden
.getVisContigsIterator(startRes, endRes + 1, true);
while (regions.hasNext())
* service</li>
* <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
* <li>RIGHT_ALIGN_IDS boolean</li>
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
* <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)</li>
* <li>VERSION_CHECK (true) check for the latest release version from
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
/**
* Sifts settings
*/
FileFormatI format = null;
DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
- Vector<String> getFeatures = null; // vector of das source nicknames to
- // fetch
- // features from
- // loading is done.
+
String groovyscript = null; // script to execute after all loading is
// completed one way or another
// extract groovy argument and execute if necessary
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
-
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures != null)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- {
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
-
- }
- }
- }
- getFeatures = null; // have retrieved features - forget them now.
- }
if (groovyscript != null)
{
// Execute the groovy script after we've done all the rendering stuff
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
- getFeatures = checkDasArguments(aparser);
// extract groovy arguments before anything else.
}
- // If the user has specified features to be retrieved,
- // or a groovy script to be executed, do them if they
- // haven't been done already
- // fetch features for the default alignment
- if (getFeatures != null)
- {
- if (startUpAlframe != null)
- {
- startFeatureFetching(getFeatures);
- }
- }
+
// Once all other stuff is done, execute any groovy scripts (in order)
if (groovyscript != null)
{
// (quote the 'PROPERTY=VALUE' pair to ensure spaces are
// passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
- + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
- + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
- + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
// +
// "-vdoc vamsas-document\tImport vamsas document into new
}
}
- /**
- * Check commandline for any das server definitions or any fetchfrom switches
- *
- * @return vector of DAS source nicknames to retrieve from
- */
- private static Vector<String> checkDasArguments(ArgsParser aparser)
- {
- Vector<String> source = null;
- String data;
- String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
- while ((data = aparser.getValue("dasserver", true)) != null)
- {
- String nickname = null;
- String url = null;
- int pos = data.indexOf('=');
- // determine capabilities
- if (pos > 0)
- {
- nickname = data.substring(0, pos);
- }
- url = data.substring(pos + 1);
- if (url != null && (url.startsWith("http:")
- || url.startsWith("sequence:http:")))
- {
- if (nickname == null)
- {
- nickname = url;
- }
- if (locsources == null)
- {
- locsources = "";
- }
- else
- {
- locsources += "\t";
- }
- locsources = locsources + nickname + "|" + url;
- System.err.println(
- "NOTE! dasserver parameter not yet really supported (got args of "
- + nickname + "|" + url);
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(nickname);
- }
- System.out.println(
- "CMD [-dasserver " + data + "] executed successfully!");
- } // loop until no more server entries are found.
- if (locsources != null && locsources.indexOf('|') > -1)
- {
- Cache.log.debug("Setting local source list in properties file to:\n"
- + locsources);
- Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
- }
- while ((data = aparser.getValue("fetchfrom", true)) != null)
- {
- System.out.println("adding source '" + data + "'");
- if (source == null)
- {
- source = new Vector<>();
- }
- source.addElement(data);
- }
- return source;
- }
-
- /**
- * start a feature fetcher for every alignment frame
- *
- * @param dasSources
- */
- private FeatureFetcher startFeatureFetching(
- final Vector<String> dasSources)
- {
- FeatureFetcher ff = new FeatureFetcher();
- AlignFrame afs[] = Desktop.getAlignFrames();
- if (afs == null || afs.length == 0)
- {
- return null;
- }
- for (int i = 0; i < afs.length; i++)
- {
- ff.addFetcher(afs[i], dasSources);
- }
- return ff;
- }
-
public static boolean isHeadlessMode()
{
String isheadless = System.getProperty("java.awt.headless");
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
+ maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
}
-
return maxLength;
}
- /*
+
@Override
- public int getWidth()
+ public int getVisibleWidth()
{
- final Wrapper temp = new Wrapper();
-
- forEachSequence(new Consumer<SequenceI>()
+ int w = getWidth();
+ if (hiddenCols != null)
{
- @Override
- public void accept(SequenceI s)
- {
- if (s.getLength() > temp.inner)
- {
- temp.inner = s.getLength();
- }
- }
- }, 0, sequences.size() - 1);
-
- return temp.inner;
+ w -= hiddenCols.getSize();
+ }
+ return w;
}
-
- public static class Wrapper
- {
- public int inner;
- }*/
/**
* DOCUMENT ME!
/**
*
- * Calculates the maximum width of the alignment, including gaps.
+ * Answers the width of the alignment, including gaps, that is, the length of
+ * the longest sequence, or -1 if there are no sequences. Avoid calling this
+ * method repeatedly where possible, as it has to perform a calculation. Note
+ * that this width includes any hidden columns.
*
- * @return Greatest sequence length within alignment, or -1 if no sequences
- * present
+ * @return
+ * @see AlignmentI#getVisibleWidth()
*/
@Override
int getWidth();
/**
+ *
+ * Answers the visible width of the alignment, including gaps, that is, the
+ * length of the longest sequence, excluding any hidden columns. Answers -1 if
+ * there are no sequences. Avoid calling this method repeatedly where
+ * possible, as it has to perform a calculation.
+ *
+ * @return
+ */
+ int getVisibleWidth();
+
+ /**
* Calculates if this set of sequences (visible and invisible) are all the
* same length
*
import java.util.BitSet;
import java.util.Collections;
import java.util.List;
+import java.util.regex.PatternSyntaxException;
/**
* Data class holding the selected columns and hidden column ranges for a view.
*/
IntList()
{
- order = new ArrayList<Integer>();
+ order = new ArrayList<>();
_uorder = Collections.unmodifiableList(order);
selected = new BitSet();
}
*/
List<int[]> getRanges()
{
- List<int[]> rlist = new ArrayList<int[]>();
+ List<int[]> rlist = new ArrayList<>();
if (selected.isEmpty())
{
return rlist;
}
}
- IntList selection = new IntList();
+ private IntList selection = new IntList();
/**
* Add a column to the selection
return (selection != null && selection.size() > 0);
}
- public boolean filterAnnotations(Annotation[] annotations,
+ /**
+ * Selects columns where the given annotation matches the provided filter
+ * condition(s). Any existing column selections are first cleared. Answers the
+ * number of columns added.
+ *
+ * @param annotations
+ * @param filterParams
+ * @return
+ */
+ public int filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
// JBPNote - this method needs to be refactored to become independent of
// viewmodel package
this.clear();
- int count = 0;
+ int addedCount = 0;
+ int column = 0;
do
{
- if (annotations[count] != null)
+ Annotation ann = annotations[column];
+ if (ann != null)
{
+ boolean matched = false;
- boolean itemMatched = false;
-
+ /*
+ * filter may have multiple conditions -
+ * these are or'd until a match is found
+ */
if (filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
- && annotations[count].value >= filterParams
- .getThresholdValue())
+ && ann.value > filterParams.getThresholdValue())
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams
+
+ if (!matched && filterParams
.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
- && annotations[count].value <= filterParams
- .getThresholdValue())
+ && ann.value < filterParams.getThresholdValue())
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterAlphaHelix()
- && annotations[count].secondaryStructure == 'H')
+ if (!matched && filterParams.isFilterAlphaHelix()
+ && ann.secondaryStructure == 'H')
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterBetaSheet()
- && annotations[count].secondaryStructure == 'E')
+ if (!matched && filterParams.isFilterBetaSheet()
+ && ann.secondaryStructure == 'E')
{
- itemMatched = true;
+ matched = true;
}
- if (filterParams.isFilterTurn()
- && annotations[count].secondaryStructure == 'S')
+ if (!matched && filterParams.isFilterTurn()
+ && ann.secondaryStructure == 'S')
{
- itemMatched = true;
+ matched = true;
}
String regexSearchString = filterParams.getRegexString();
- if (regexSearchString != null
- && !filterParams.getRegexSearchFields().isEmpty())
+ if (!matched && regexSearchString != null)
{
List<SearchableAnnotationField> fields = filterParams
.getRegexSearchFields();
- try
+ for (SearchableAnnotationField field : fields)
{
- if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
- && annotations[count].displayCharacter
- .matches(regexSearchString))
+ String compareTo = field == SearchableAnnotationField.DISPLAY_STRING
+ ? ann.displayCharacter // match 'Label'
+ : ann.description; // and/or 'Description'
+ if (compareTo != null)
{
- itemMatched = true;
- }
- } catch (java.util.regex.PatternSyntaxException pse)
- {
- if (annotations[count].displayCharacter
- .equals(regexSearchString))
- {
- itemMatched = true;
+ try
+ {
+ if (compareTo.matches(regexSearchString))
+ {
+ matched = true;
+ }
+ } catch (PatternSyntaxException pse)
+ {
+ if (compareTo.equals(regexSearchString))
+ {
+ matched = true;
+ }
+ }
+ if (matched)
+ {
+ break;
+ }
}
}
- if (fields.contains(SearchableAnnotationField.DESCRIPTION)
- && annotations[count].description != null
- && annotations[count].description
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
}
- if (itemMatched)
+ if (matched)
{
- this.addElement(count);
+ this.addElement(column);
+ addedCount++;
}
}
- count++;
- } while (count < annotations.length);
- return false;
+ column++;
+ } while (column < annotations.length);
+
+ return addedCount;
}
/**
*/
int getEnd();
+ /**
+ * Answers true if this match is for the given sequence and includes (matches
+ * or encloses) the given start-end range
+ *
+ * @param seq
+ * @param start
+ * @param end
+ * @return
+ */
+ boolean contains(SequenceI seq, int start, int end);
}
\ No newline at end of file
}
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getSequence()
- */
@Override
public SequenceI getSequence()
{
return sequence;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getStart()
- */
@Override
public int getStart()
{
return start;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getEnd()
- */
@Override
public int getEnd()
{
return (sequence == m.getSequence() && start == m.getStart()
&& end == m.getEnd());
}
+
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
+ }
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
- */
@Override
public SearchResultMatchI addResult(SequenceI seq, int start, int end)
{
Match m = new Match(seq, start, end);
- matches.add(m);
+ if (!matches.contains(m))
+ {
+ matches.add(m);
+ }
return m;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
- */
@Override
public boolean involvesSequence(SequenceI sequence)
{
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
- */
@Override
public int[] getResults(SequenceI sequence, int start, int end)
{
return count;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getSize()
- */
@Override
public int getSize()
{
return matches.size();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#isEmpty()
- */
@Override
public boolean isEmpty()
{
return matches.isEmpty();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults()
- */
@Override
public List<SearchResultMatchI> getResults()
{
{
/**
- * Adds one region to the results
+ * Adds one region to the results (unless already added, to avoid duplicates)
*
* @param seq
- * Sequence
* @param start
- * int
* @param end
- * int
* @return
*/
SearchResultMatchI addResult(SequenceI seq, int start, int end);
* get a range on the sequence as a string
*
* @param start
- * position relative to start of sequence including gaps (from 0)
+ * (inclusive) position relative to start of sequence including gaps
+ * (from 0)
* @param end
- * position relative to start of sequence including gaps (from 0)
+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
*
* @return String containing all gap and symbols in specified range
*/
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
+import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
@SuppressWarnings("serial")
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
+ private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
+
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
Integer height = getTempUserPrefs().get("FTSPanel.height") == null ? 400
: getTempUserPrefs().get("FTSPanel.height");
lbl_warning.setVisible(false);
- lbl_warning.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_warning.setFont(VERDANA_12);
lbl_loading.setVisible(false);
- lbl_loading.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_loading.setFont(VERDANA_12);
lbl_blank.setVisible(true);
- lbl_blank.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_blank.setFont(VERDANA_12);
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
}
});
+ JButton txt_help = new JButton("?");
+ txt_help.setFont(VERDANA_12);
+ txt_help.setPreferredSize(new Dimension(15, 15));
+ txt_help.setToolTipText(MessageManager.getString("action.help"));
+ txt_help.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHelp();
+ }
+ });
+
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
Boolean.toString(btn_autosearch.isSelected()));
}
});
- btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_back.setFont(VERDANA_12);
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
{
});
btn_ok.setEnabled(false);
- btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setFont(VERDANA_12);
btn_ok.setText(MessageManager.getString("action.ok"));
btn_ok.addActionListener(new java.awt.event.ActionListener()
{
btn_next_page.setEnabled(false);
btn_next_page.setToolTipText(
MessageManager.getString("label.next_page_tooltip"));
- btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_next_page.setFont(VERDANA_12);
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
{
btn_prev_page.setEnabled(false);
btn_prev_page.setToolTipText(
MessageManager.getString("label.prev_page_tooltip"));
- btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_prev_page.setFont(VERDANA_12);
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
{
btn_next_page.setVisible(false);
}
- btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setFont(VERDANA_12);
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
{
});
scrl_searchResult.setPreferredSize(new Dimension(width, height));
- cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_searchTarget.setFont(VERDANA_12);
cmb_searchTarget.addItemListener(new ItemListener()
{
@Override
}
});
- txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
+ txt_search.setFont(VERDANA_12);
txt_search.getEditor().getEditorComponent()
.addKeyListener(new KeyAdapter()
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
+ pnl_inputs.add(txt_help);
pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), width, height);
}
+ abstract protected void showHelp();
+
protected void closeAction()
{
getTempUserPrefs().put("FTSPanel.width", this.getWidth());
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
{
return PDB_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.PdbFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
\ No newline at end of file
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
{
return UNIPROT_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.UniprotFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingI;
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- // reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(width);
- }
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- final int alignmentWidth = av.getAlignment().getWidth();
- final int pagesWide = (alignmentWidth / totalRes) + 1;
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
final int startRes = (pageIndex % pagesWide) * totalRes;
final int endRes = Math.min(startRes + totalRes - 1,
int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int resWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(pageWidth - idWidth);
public AlignmentDimension getAlignmentDimension()
{
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
}
}
});
+ searchBox.getEditor().getEditorComponent()
+ .addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ searchStringAction();
+ }
+ });
JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- discriptionCheckboxAction();
+ descriptionCheckboxAction();
}
});
aColChooser.updateView();
}
- public void discriptionCheckboxAction()
+ public void descriptionCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
MouseListener, MouseWheelListener, MouseMotionListener,
ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
{
+ enum DragMode
+ {
+ Select, Resize, Undefined
+ };
+
String HELIX = MessageManager.getString("label.helix");
String SHEET = MessageManager.getString("label.sheet");
// Used For mouse Dragging and resizing graphs
int graphStretch = -1;
- int graphStretchY = -1;
+ int mouseDragLastX = -1;
- int min; // used by mouseDragged to see if user
+ int mouseDragLastY = -1;
- int max; // used by mouseDragged to see if user
+ DragMode dragMode = DragMode.Undefined;
boolean mouseDragging = false;
}
/**
- * DOCUMENT ME!
+ * Action on right mouse pressed on Mac is to show a pop-up menu for the
+ * annotation. Action on left mouse pressed is to find which annotation is
+ * pressed and mark the start of a column selection or graph resize operation.
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mousePressed(MouseEvent evt)
{
return;
}
+ mouseDragLastX = evt.getX();
+ mouseDragLastY = evt.getY();
+ /*
+ * add visible annotation heights until we reach the y
+ * position, to find which annotation it is in
+ */
int height = 0;
activeRow = -1;
}
else if (aa[i].graph > 0)
{
- // Stretch Graph
+ /*
+ * we have clicked on a resizable graph annotation
+ */
graphStretch = i;
- graphStretchY = y;
}
-
break;
}
}
}
/**
- * DOCUMENT ME!
+ * Action on mouse up is to clear mouse drag data and call mouseReleased on
+ * ScalePanel, to deal with defining the selection group (if any) defined by
+ * the mouse drag
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
- graphStretchY = -1;
+ mouseDragLastX = -1;
+ mouseDragLastY = -1;
mouseDragging = false;
+ dragMode = DragMode.Undefined;
ap.getScalePanel().mouseReleased(evt);
/*
@Override
public void mouseDragged(MouseEvent evt)
{
- if (graphStretch > -1)
+ /*
+ * todo: if dragMode is Undefined:
+ * - set to Select if dx > dy
+ * - set to Resize if dy > dx
+ * - do nothing if dx == dy
+ */
+ final int x = evt.getX();
+ final int y = evt.getY();
+ if (dragMode == DragMode.Undefined)
{
- av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- - evt.getY();
- if (av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ int dx = Math.abs(x - mouseDragLastX);
+ int dy = Math.abs(y - mouseDragLastY);
+ if (graphStretch == -1 || dx > dy)
{
- av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ /*
+ * mostly horizontal drag, or not a graph annotation
+ */
+ dragMode = DragMode.Select;
+ }
+ else if (dy > dx)
+ {
+ /*
+ * mostly vertical drag
+ */
+ dragMode = DragMode.Resize;
}
- graphStretchY = evt.getY();
- adjustPanelHeight();
- ap.paintAlignment(false, false);
}
- else
+
+ if (dragMode == DragMode.Undefined)
+ {
+ /*
+ * drag is diagonal - defer deciding whether to
+ * treat as up/down or left/right
+ */
+ return;
+ }
+
+ try
+ {
+ if (dragMode == DragMode.Resize)
+ {
+ /*
+ * resize graph annotation if mouse was dragged up or down
+ */
+ int deltaY = mouseDragLastY - evt.getY();
+ if (deltaY != 0)
+ {
+ AlignmentAnnotation graphAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch];
+ int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
+ graphAnnotation.graphHeight = newHeight;
+ adjustPanelHeight();
+ ap.paintAlignment(false, false);
+ }
+ }
+ else
+ {
+ /*
+ * for mouse drag left or right, delegate to
+ * ScalePanel to adjust the column selection
+ */
+ ap.getScalePanel().mouseDragged(evt);
+ }
+ } finally
{
- ap.getScalePanel().mouseDragged(evt);
+ mouseDragLastX = x;
+ mouseDragLastY = y;
}
}
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import javax.swing.JTable;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
+import javax.swing.border.Border;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.table.AbstractTableModel;
private static final int MIN_HEIGHT = 400;
+ private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+
final FeatureRenderer fr;
public final AlignFrame af;
int selectedRow = -1;
- JButton fetchDAS = new JButton();
-
- JButton saveDAS = new JButton();
-
- JButton cancelDAS = new JButton();
-
boolean resettingTable = false;
/*
{
String tip = null;
int column = table.columnAtPoint(e.getPoint());
+ int row = table.rowAtPoint(e.getPoint());
+
switch (column)
{
case TYPE_COLUMN:
tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
break;
+ case COLOUR_COLUMN:
+ FeatureColourI colour = (FeatureColourI) table.getValueAt(row,
+ column);
+ tip = getColorTooltip(colour, true);
+ break;
case FILTER_COLUMN:
- int row = table.rowAtPoint(e.getPoint());
FeatureMatcherSet o = (FeatureMatcherSet) table.getValueAt(row,
column);
tip = o.isEmpty()
default:
break;
}
+
return tip;
}
+
+ /**
+ * Position the tooltip near the bottom edge of, and half way across, the
+ * current cell
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent e)
+ {
+ Point point = e.getPoint();
+ int column = table.columnAtPoint(point);
+ int row = table.rowAtPoint(point);
+ Rectangle r = getCellRect(row, column, false);
+ Point loc = new Point(r.x + r.width / 2, r.y + r.height - 3);
+ return loc;
+ }
};
JTableHeader tableHeader = table.getTableHeader();
tableHeader.setFont(new Font("Verdana", Font.PLAIN, 12));
tableHeader.setReorderingAllowed(false);
table.setFont(new Font("Verdana", Font.PLAIN, 12));
- // table.setDefaultRenderer(Color.class, new ColorRenderer());
- // table.setDefaultEditor(Color.class, new ColorEditor(this));
- //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
}
}
});
- help.setFont(JvSwingUtils.getLabelFont());
- help.setText(MessageManager.getString("action.help"));
- help.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
- Help.showHelpWindow(HelpId.SequenceFeatureSettings);
- } catch (HelpSetException e1)
- {
- e1.printStackTrace();
- }
- }
- });
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(JvSwingUtils.getLabelFont());
this.add(settingsPane);
}
+ /**
+ * Answers a suitable tooltip to show on the colour cell of the table
+ *
+ * @param fcol
+ * @param withHint
+ * if true include 'click to edit' and similar text
+ * @return
+ */
+ public static String getColorTooltip(FeatureColourI fcol,
+ boolean withHint)
+ {
+ if (fcol == null)
+ {
+ return null;
+ }
+ if (fcol.isSimpleColour())
+ {
+ return withHint ? BASE_TOOLTIP : null;
+ }
+ String description = fcol.getDescription();
+ description = description.replaceAll("<", "<");
+ description = description.replaceAll(">", ">");
+ StringBuilder tt = new StringBuilder(description);
+ if (withHint)
+ {
+ tt.append("<br>").append(BASE_TOOLTIP).append("</br>");
+ }
+ return JvSwingUtils.wrapTooltip(true, tt.toString());
+ }
+
+ public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
+ int w, int h)
+ {
+ boolean thr = false;
+ StringBuilder tx = new StringBuilder();
+
+ if (gcol.isColourByAttribute())
+ {
+ tx.append(FeatureMatcher
+ .toAttributeDisplayName(gcol.getAttributeName()));
+ }
+ else if (!gcol.isColourByLabel())
+ {
+ tx.append(MessageManager.getString("label.score"));
+ }
+ tx.append(" ");
+ if (gcol.isAboveThreshold())
+ {
+ thr = true;
+ tx.append(">");
+ }
+ if (gcol.isBelowThreshold())
+ {
+ thr = true;
+ tx.append("<");
+ }
+ if (gcol.isColourByLabel())
+ {
+ if (thr)
+ {
+ tx.append(" ");
+ }
+ if (!gcol.isColourByAttribute())
+ {
+ tx.append("Label");
+ }
+ comp.setIcon(null);
+ }
+ else
+ {
+ Color newColor = gcol.getMaxColour();
+ comp.setBackground(newColor);
+ // System.err.println("Width is " + w / 2);
+ Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
+ comp.setIcon(ficon);
+ // tt+="RGB value: Max (" + newColor.getRed() + ", "
+ // + newColor.getGreen() + ", " + newColor.getBlue()
+ // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
+ // + ", " + minCol.getBlue() + ")");
+ }
+ comp.setHorizontalAlignment(SwingConstants.CENTER);
+ comp.setText(tx.toString());
+ }
+
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
class ColorRenderer extends JLabel implements TableCellRenderer
{
- javax.swing.border.Border unselectedBorder = null;
+ Border unselectedBorder = null;
- javax.swing.border.Border selectedBorder = null;
-
- final String baseTT = "Click to edit, right/apple click for menu.";
+ Border selectedBorder = null;
public ColorRenderer()
{
{
FeatureColourI cellColour = (FeatureColourI) color;
setOpaque(true);
- setToolTipText(baseTT);
setBackground(tbl.getBackground());
if (!cellColour.isSimpleColour())
{
renderGraduatedColor(comp, gcol, w, h);
}
- public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
- int w, int h)
- {
- boolean thr = false;
- StringBuilder tt = new StringBuilder();
- StringBuilder tx = new StringBuilder();
-
- if (gcol.isColourByAttribute())
- {
- tx.append(String.join(":", gcol.getAttributeName()));
- }
- else if (!gcol.isColourByLabel())
- {
- tx.append(MessageManager.getString("label.score"));
- }
- tx.append(" ");
- if (gcol.isAboveThreshold())
- {
- thr = true;
- tx.append(">");
- tt.append("Thresholded (Above ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isBelowThreshold())
- {
- thr = true;
- tx.append("<");
- tt.append("Thresholded (Below ").append(gcol.getThreshold())
- .append(") ");
- }
- if (gcol.isColourByLabel())
- {
- tt.append("Coloured by label text. ").append(tt);
- if (thr)
- {
- tx.append(" ");
- }
- if (!gcol.isColourByAttribute())
- {
- tx.append("Label");
- }
- comp.setIcon(null);
- }
- else
- {
- Color newColor = gcol.getMaxColour();
- comp.setBackground(newColor);
- // System.err.println("Width is " + w / 2);
- Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
- comp.setIcon(ficon);
- // tt+="RGB value: Max (" + newColor.getRed() + ", "
- // + newColor.getGreen() + ", " + newColor.getBlue()
- // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
- // + ", " + minCol.getBlue() + ")");
- }
- comp.setHorizontalAlignment(SwingConstants.CENTER);
- comp.setText(tx.toString());
- if (tt.length() > 0)
- {
- if (comp.getToolTipText() == null)
- {
- comp.setToolTipText(tt.toString());
- }
- else
- {
- comp.setToolTipText(
- tt.append(" ").append(comp.getToolTipText()).toString());
- }
- }
- }
-
class ColorEditor extends AbstractCellEditor
implements TableCellEditor, ActionListener
{
button.setOpaque(true);
button.setBackground(me.getBackground());
button.setText(currentFilter.toString());
- button.setToolTipText(currentFilter.toString());
button.setIcon(null);
return button;
}
maxColour.setBorder(new LineBorder(Color.black));
/*
- * default max colour to last plain colour;
- * make min colour a pale version of max colour
+ * if not set, default max colour to last plain colour,
+ * and make min colour a pale version of max colour
*/
- FeatureColourI fc = fr.getFeatureColours().get(featureType);
- Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
- maxColour.setBackground(bg);
- minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
+ Color max = originalColour.getMaxColour();
+ if (max == null)
+ {
+ max = originalColour.getColour();
+ minColour.setBackground(ColorUtils.bleachColour(max, 0.9f));
+ }
+ else
+ {
+ maxColour.setBackground(max);
+ minColour.setBackground(originalColour.getMinColour());
+ }
noValueCombo = new JComboBox<>();
noValueCombo.addItem(MessageManager.getString("label.no_colour"));
singleColour.setFont(JvSwingUtils.getLabelFont());
singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
singleColour.setPreferredSize(new Dimension(40, 20));
- if (originalColour.isGraduatedColour())
- {
- singleColour.setBackground(originalColour.getMaxColour());
- singleColour.setForeground(originalColour.getMaxColour());
- }
- else
- {
+ // if (originalColour.isGraduatedColour())
+ // {
+ // singleColour.setBackground(originalColour.getMaxColour());
+ // singleColour.setForeground(originalColour.getMaxColour());
+ // }
+ // else
+ // {
singleColour.setBackground(originalColour.getColour());
singleColour.setForeground(originalColour.getColour());
- }
+ // }
singleColour.addMouseListener(new MouseAdapter()
{
@Override
private FeatureColourI makeColourFromInputs()
{
/*
- * easiest case - a single colour
+ * min-max range is to (or from) threshold value if
+ * 'threshold is min/max' is selected
*/
- if (simpleColour.isSelected())
- {
- return new FeatureColour(singleColour.getBackground());
- }
-
- /*
- * next easiest case - colour by Label, or attribute text
- */
- if (byCategory.isSelected())
- {
- Color c = singleColour.getBackground();
- FeatureColourI fc = new FeatureColour(c);
- fc.setColourByLabel(true);
- String byWhat = (String) colourByTextCombo.getSelectedItem();
- if (!LABEL_18N.equals(byWhat))
- {
- fc.setAttributeName(
- FeatureMatcher.fromAttributeDisplayName(byWhat));
- }
- return fc;
- }
-
- /*
- * remaining case - graduated colour by score, or attribute value
- */
- Color noColour = null;
- if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
- {
- noColour = minColour.getBackground();
- }
- else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
- {
- noColour = maxColour.getBackground();
- }
float thresh = 0f;
try
{
// invalid inputs are already handled on entry
}
-
- /*
- * min-max range is to (or from) threshold value if
- * 'threshold is min/max' is selected
- */
float minValue = min;
float maxValue = max;
final int thresholdOption = threshold.getSelectedIndex();
{
maxValue = thresh;
}
+ Color noColour = null;
+ if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
+ {
+ noColour = minColour.getBackground();
+ }
+ else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
+ {
+ noColour = maxColour.getBackground();
+ }
+
+ /*
+ * construct a colour that 'remembers' all the options, including
+ * those not currently selected
+ */
+ FeatureColourI fc = new FeatureColour(singleColour.getBackground(),
+ minColour.getBackground(), maxColour.getBackground(), noColour,
+ minValue, maxValue);
+
+ /*
+ * easiest case - a single colour
+ */
+ if (simpleColour.isSelected())
+ {
+ ((FeatureColour) fc).setGraduatedColour(false);
+ return fc;
+ }
/*
- * make the graduated colour
+ * next easiest case - colour by Label, or attribute text
*/
- FeatureColourI fc = new FeatureColour(minColour.getBackground(),
- maxColour.getBackground(), noColour, minValue, maxValue);
+ if (byCategory.isSelected())
+ {
+ fc.setColourByLabel(true);
+ String byWhat = (String) colourByTextCombo.getSelectedItem();
+ if (!LABEL_18N.equals(byWhat))
+ {
+ fc.setAttributeName(
+ FeatureMatcher.fromAttributeDisplayName(byWhat));
+ }
+ return fc;
+ }
/*
+ * remaining case - graduated colour by score, or attribute value;
* set attribute to colour by if selected
*/
String byWhat = (String) colourByRangeCombo.getSelectedItem();
*/
package jalview.gui;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
+import java.util.Map;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
/**
*/
public class Finder extends GFinder
{
- private static final int MY_HEIGHT = 120;
+ private static final int MIN_WIDTH = 350;
- private static final int MY_WIDTH = 400;
+ private static final int MIN_HEIGHT = 120;
- AlignmentViewport av;
+ private static final int MY_HEIGHT = 120;
- AlignmentPanel ap;
+ private static final int MY_WIDTH = 400;
- private static final int MIN_WIDTH = 350;
+ private AlignViewportI av;
- private static final int MIN_HEIGHT = 120;
+ private AlignmentPanel ap;
- JInternalFrame frame;
+ private JInternalFrame frame;
- int seqIndex = 0;
+ /*
+ * Finder agent per viewport searched
+ */
+ private Map<AlignViewportI, FinderI> finders;
- int resIndex = -1;
+ private SearchResultsI searchResults;
- SearchResultsI searchResults;
+ /*
+ * true if we only search a given alignment view
+ */
+ private boolean focusfixed;
/**
- * Creates a new Finder object with no associated viewport or panel.
+ * Creates a new Finder object with no associated viewport or panel. Each Find
+ * or Find Next action will act on whichever viewport has focus at the time.
*/
public Finder()
{
this(null, null);
- focusfixed = false;
}
/**
{
av = viewport;
ap = alignPanel;
- focusfixed = true;
+ finders = new HashMap<>();
+ focusfixed = viewport != null;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
- new javax.swing.event.InternalFrameAdapter()
+ new InternalFrameAdapter()
{
@Override
public void internalFrameClosing(InternalFrameEvent e)
}
/**
- * Performs the 'Find Next' action.
- *
- * @param e
+ * Performs the 'Find Next' action on the alignment panel with focus
*/
@Override
- public void findNext_actionPerformed(ActionEvent e)
+ public void findNext_actionPerformed()
{
if (getFocusedViewport())
{
}
/**
- * Performs the 'Find All' action.
- *
- * @param e
+ * Performs the 'Find All' action on the alignment panel with focus
*/
@Override
- public void findAll_actionPerformed(ActionEvent e)
+ public void findAll_actionPerformed()
{
if (getFocusedViewport())
{
- resIndex = -1;
- seqIndex = 0;
doSearch(true);
}
}
/**
- * do we only search a given alignment view ?
- */
- private boolean focusfixed;
-
- /**
* if !focusfixed and not in a desktop environment, checks that av and ap are
* valid. Otherwise, gets the topmost alignment window and sets av and ap
* accordingly
for (int f = 0; f < frames.length; f++)
{
JInternalFrame alignFrame = frames[f];
- if (alignFrame != null && alignFrame instanceof AlignFrame)
+ if (alignFrame != null && alignFrame instanceof AlignFrame
+ && !alignFrame.isIcon())
{
av = ((AlignFrame) alignFrame).viewport;
ap = ((AlignFrame) alignFrame).alignPanel;
@Override
public void createFeatures_actionPerformed()
{
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
String searchString = searchBox.getEditor().getItem().toString().trim();
String desc = "Search Results";
// other stuff
// TODO: add switches to control what is searched - sequences, IDS,
// descriptions, features
- jalview.analysis.Finder finder = new jalview.analysis.Finder(
- av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
- finder.setCaseSensitive(caseSensitive.isSelected());
- finder.setIncludeDescription(searchDescription.isSelected());
-
- finder.setFindAll(doFindAll);
-
- finder.find(searchString); // returns true if anything was actually found
-
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we've searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
- searchResults = finder.getSearchResults(); // find(regex,
- // caseSensitive.isSelected(), )
- Vector<SequenceI> idMatch = finder.getIdMatch();
- boolean haveResults = false;
- // set or reset the GUI
- if ((idMatch.size() > 0))
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ if (doFindAll)
{
- haveResults = true;
- ap.getIdPanel().highlightSearchResults(idMatch);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
- ap.getIdPanel().highlightSearchResults(null);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
- if (searchResults.getSize() > 0)
+ searchResults = finder.getSearchResults();
+ List<SequenceI> idMatch = finder.getIdMatches();
+ ap.getIdPanel().highlightSearchResults(idMatch);
+
+ if (searchResults.isEmpty())
{
- haveResults = true;
- createFeatures.setEnabled(true);
+ searchResults = null;
}
else
{
- searchResults = null;
+ createFeatures.setEnabled(true);
}
- // if allResults is null, this effectively switches displaySearch flag in
- // seqCanvas
ap.highlightSearchResults(searchResults);
// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
// 'SelectRegion' selection
- if (!haveResults)
+ if (idMatch.isEmpty() && searchResults == null)
{
JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
else
{
}
JvOptionPane.showInternalMessageDialog(this, message, null,
JvOptionPane.INFORMATION_MESSAGE);
- resIndex = -1;
- seqIndex = 0;
}
}
searchBox.updateCache();
*/
package jalview.gui;
+import java.awt.Point;
import java.net.URL;
import javax.help.BadIDException;
import javax.help.HelpSetException;
/**
- * Utility class to show the help documentation window.
+ * Utility class to show the help documentation window
*
* @author gmcarstairs
- *
*/
public class Help
{
public enum HelpId
{
Home("home"), SequenceFeatureSettings("seqfeatures.settings"),
- StructureViewer("viewingpdbs");
+ StructureViewer("viewingpdbs"), PdbFts("pdbfts"),
+ UniprotFts("uniprotfts");
private String id;
}
}
- private static final long HALF_A_MO = 500; // half a second
-
- private static long lastOpenedTime = 0L;
+ private static HelpBroker hb;
/**
* Not instantiable
}
/**
- * Show help text in a new window. But do nothing if within half a second of
- * the last invocation.
- *
- * This is a workaround for issue JAL-914 - both Desktop and AlignFrame
- * responding to F1 key, resulting in duplicate help windows opened.
+ * Shows the help window, at the entry specified by the given helpId
*
* @param id
- * TODO
*
* @throws HelpSetException
*/
public static void showHelpWindow(HelpId id) throws HelpSetException
{
- long timeNow = System.currentTimeMillis();
+ ClassLoader cl = Desktop.class.getClassLoader();
+ URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
+ HelpSet hs = new HelpSet(cl, url);
- if (timeNow - lastOpenedTime > HALF_A_MO)
+ if (hb == null)
{
- lastOpenedTime = timeNow;
- ClassLoader cl = Desktop.class.getClassLoader();
- URL url = HelpSet.findHelpSet(cl, "help/help"); // $NON-NLS-$
- HelpSet hs = new HelpSet(cl, url);
+ /*
+ * create help broker first time (only)
+ */
+ hb = hs.createHelpBroker();
+ }
- HelpBroker hb = hs.createHelpBroker();
- try
- {
- hb.setCurrentID(id.toString());
- } catch (BadIDException bad)
- {
- System.out.println("Bad help link: " + id.toString()
- + ": must match a target in help.jhm");
- throw bad;
- }
- hb.setDisplayed(true);
+ try
+ {
+ hb.setCurrentID(id.toString());
+ } catch (BadIDException bad)
+ {
+ System.out.println("Bad help link: " + id.toString()
+ + ": must match a target in help.jhm");
+ throw bad;
}
+
+ /*
+ * set Help visible - at its current location if it is already shown,
+ * else at a location as determined by the window manager
+ */
+ Point p = hb.getLocation();
+ hb.setLocation(p);
+ hb.setDisplayed(true);
}
+ /**
+ * Show the Help window at the root entry
+ *
+ * @throws HelpSetException
+ */
public static void showHelpWindow() throws HelpSetException
{
showHelpWindow(HelpId.Home);
int alignmentWidth = alignViewport.getAlignment().getWidth();
final int alheight = alignViewport.getAlignment().getHeight();
- if (alignViewport.hasHiddenColumns())
- {
- alignmentWidth = alignViewport.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(alignmentWidth) - 1;
- }
-
int annotationHeight = 0;
AnnotationLabels labels = null;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
}
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
{
getIdCanvas().setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
this.idCanvas = idCanvas;
}
- // this class allows scrolling off the bottom of the visible alignment
+ /**
+ * Performs scrolling of the visible alignment up or down, adding newly
+ * visible sequences to the current selection
+ */
class ScrollThread extends Thread
{
- boolean running = false;
+ private boolean running = false;
- boolean up = true;
+ private boolean up;
+ /**
+ * Constructor for a thread that scrolls either up or down
+ *
+ * @param up
+ */
public ScrollThread(boolean up)
{
this.up = up;
+ setName("IdPanel$ScrollThread$" + String.valueOf(up));
start();
}
+ /**
+ * Sets a flag to stop the scrolling
+ */
public void stopScrolling()
{
running = false;
}
+ /**
+ * Scrolls the alignment either up or down, one row at a time, adding newly
+ * visible sequences to the current selection. Speed is limited to a maximum
+ * of ten rows per second. The thread exits when the end of the alignment is
+ * reached or a flag is set to stop it.
+ */
@Override
public void run()
{
while (running)
{
- if (av.getRanges().scrollUp(up))
+ ViewportRanges ranges = IdPanel.this.av.getRanges();
+ if (ranges.scrollUp(up))
{
- // scroll was ok, so add new sequence to selection
- int seq = av.getRanges().getStartSeq();
-
- if (!up)
- {
- seq = av.getRanges().getEndSeq();
- }
-
- if (seq < lastid)
- {
- selectSeqs(lastid - 1, seq);
- }
- else if (seq > lastid)
- {
- selectSeqs(lastid + 1, seq);
- }
-
- lastid = seq;
+ int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+ int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+ IdPanel.this.selectSeqs(fromSeq, toSeq);
+
+ lastid = toSeq;
}
else
{
+ /*
+ * scroll did nothing - reached limit of visible alignment
+ */
running = false;
}
// without this the overview window does not size to fit the overview canvas
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
+
addComponentListener(new ComponentAdapter()
{
@Override
@Override
public void mouseMoved(MouseEvent evt)
{
- if (!draggingBox)
- // don't bother changing the cursor if we're dragging the box
- // as we can't have moved inside or out of the box in that case
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
{
- if (od.isPositionInBox(evt.getX(), evt.getY()))
- {
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- }
- else
- {
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
- }
+ /*
+ * using HAND_CURSOR rather than DRAG_CURSOR
+ * as the latter is not supported on Mac
+ */
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
+
});
addMouseListener(new MouseAdapter()
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
}
else
{
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.Point;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
protected void rightMouseButtonPressed(MouseEvent evt, final int res)
{
JPopupMenu pop = new JPopupMenu();
- if (reveal != null)
+
+ /*
+ * grab the hidden range in case mouseMoved nulls it
+ */
+ final int[] hiddenRange = reveal;
+ if (hiddenRange != null)
{
JMenuItem item = new JMenuItem(
MessageManager.getString("label.reveal"));
@Override
public void actionPerformed(ActionEvent e)
{
- av.showColumn(reveal[0]);
+ av.showColumn(hiddenRange[0]);
reveal = null;
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
{
av.showAllHiddenColumns();
reveal = null;
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
av.setSelectionGroup(null);
}
+ ap.updateLayout();
ap.paintAlignment(true, true);
av.sendSelection();
}
}
/**
- * DOCUMENT ME!
+ * Action on mouseUp is to set the limit of the current selection group (if
+ * there is one) and broadcast the selection
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
+ ap.getSeqPanel().stopScrolling();
int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
-
int res = (xCords / av.getCharWidth())
+ av.getRanges().getStartRes();
-
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
.visibleToAbsoluteColumn(res);
}
-
- if (res >= av.getAlignment().getWidth())
- {
- res = av.getAlignment().getWidth() - 1;
- }
+ res = Math.min(res, av.getAlignment().getWidth() - 1);
if (!stretchingGroup)
{
{
if (mouseDragging)
{
- ap.getSeqPanel().scrollCanvas(null);
+ ap.getSeqPanel().stopScrolling();
}
}
+ /**
+ * Action on leaving the panel bounds with mouse drag in progress is to start
+ * scrolling the alignment in the direction of the mouse. To restrict
+ * scrolling to left-right (not up-down), the y-value of the mouse position is
+ * replaced with zero.
+ */
@Override
public void mouseExited(MouseEvent evt)
{
if (mouseDragging)
{
- ap.getSeqPanel().scrollCanvas(evt);
+ ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0));
}
}
int startx = startRes;
int endx;
int ypos = hgap; // vertical offset
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth);
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
// chop the wrapped alignment extent up into panel-sized blocks and treat
// each block as if it were a block from an unwrapped alignment
}
ViewportRanges vpRanges = av.getRanges();
- int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
if (scrollX > range)
{
scrollX = range;
{
ViewportRanges ranges = av.getRanges();
- if (Math.abs(scrollX) > ranges.getViewportWidth())
+ if (Math.abs(scrollX) >= ranges.getViewportWidth())
{
/*
- * shift of more than one view width is
+ * shift of one view width or more is
* overcomplicated to handle in this method
*/
fastPaint = false;
while (y >= 0)
{
+ /*
+ * shift 'widthToCopy' residues by 'positions' places to the right
+ */
gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
positions * charWidth, 0);
if (y > 0)
{
+ /*
+ * copy 'positions' residue from the row above (right hand end)
+ * to this row's left hand end
+ */
gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
positions * charWidth, heightToCopy, -widthToCopy,
wrappedRepeatHeightPx);
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
return;
}
- if (!editingSeqs)
+ if (editingSeqs)
+ {
+ endEditing();
+ }
+ else
{
doMouseReleasedDefineMode(evt, didDrag);
- return;
}
-
- endEditing();
}
/**
}
mouseDragging = true;
- if ((scrollThread != null) && (scrollThread.isRunning()))
+ if (scrollThread != null)
{
- scrollThread.setEvent(evt);
+ scrollThread.setMousePosition(evt.getPoint());
}
}
}
/**
- * DOCUMENT ME!
+ * On reentering the panel, stops any scrolling that was started on dragging
+ * out of the panel
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent e)
{
oldSeq = 0;
}
-
- if ((scrollThread != null) && (scrollThread.isRunning()))
- {
- scrollThread.stopScrolling();
- scrollThread = null;
- }
+ stopScrolling();
}
/**
- * DOCUMENT ME!
+ * On leaving the panel, if the mouse is being dragged, starts a thread to
+ * scroll it until the mouse is released (in unwrapped mode only)
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent e)
return;
}
- if (res >= av.getAlignment().getWidth())
- {
- res = av.getAlignment().getWidth() - 1;
- }
+ res = Math.min(res, av.getAlignment().getWidth()-1);
if (stretchGroup.getEndRes() == res)
{
mouseDragging = true;
- if ((scrollThread != null) && (scrollThread.isRunning()))
+ if (scrollThread != null)
{
- scrollThread.setEvent(evt);
+ scrollThread.setMousePosition(evt.getPoint());
}
/*
ap.alignFrame.setStatus(status.toString());
}
- void scrollCanvas(MouseEvent evt)
+ /**
+ * Stops the scroll thread if it is running
+ */
+ void stopScrolling()
{
- if (evt == null)
+ if (scrollThread != null)
{
- if ((scrollThread != null) && (scrollThread.isRunning()))
- {
- scrollThread.stopScrolling();
- scrollThread = null;
- }
- mouseDragging = false;
+ scrollThread.stopScrolling();
+ scrollThread = null;
}
- else
- {
- if (scrollThread == null)
- {
- scrollThread = new ScrollThread();
- }
+ mouseDragging = false;
+ }
- mouseDragging = true;
- scrollThread.setEvent(evt);
+ /**
+ * Starts a thread to scroll the alignment, towards a given mouse position
+ * outside the panel bounds
+ *
+ * @param mousePos
+ */
+ void startScrolling(Point mousePos)
+ {
+ if (scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
}
+ mouseDragging = true;
+ scrollThread.setMousePosition(mousePos);
}
- // this class allows scrolling off the bottom of the visible alignment
+ /**
+ * Performs scrolling of the visible alignment left, right, up or down
+ */
class ScrollThread extends Thread
{
- MouseEvent evt;
+ private Point mousePos;
private volatile boolean threadRunning = true;
+ /**
+ * Constructor
+ */
public ScrollThread()
{
+ setName("SeqPanel$ScrollThread");
start();
}
- public void setEvent(MouseEvent e)
+ /**
+ * Sets the position of the mouse that determines the direction of the
+ * scroll to perform
+ *
+ * @param p
+ */
+ public void setMousePosition(Point p)
{
- evt = e;
+ mousePos = p;
}
+ /**
+ * Sets a flag that will cause the thread to exit
+ */
public void stopScrolling()
{
threadRunning = false;
}
- public boolean isRunning()
- {
- return threadRunning;
- }
-
+ /**
+ * Scrolls the alignment left or right, and/or up or down, depending on the
+ * last notified mouse position, until the limit of the alignment is
+ * reached, or a flag is set to stop the scroll
+ */
@Override
public void run()
{
- while (threadRunning)
+ while (threadRunning && mouseDragging)
{
- if (evt != null)
+ if (mousePos != null)
{
- if (mouseDragging && (evt.getY() < 0)
- && (av.getRanges().getStartSeq() > 0))
+ boolean scrolled = false;
+ ViewportRanges ranges = SeqPanel.this.av.getRanges();
+
+ /*
+ * scroll up or down
+ */
+ if (mousePos.y < 0)
{
- av.getRanges().scrollUp(true);
+ // mouse is above this panel - try scroll up
+ scrolled = ranges.scrollUp(true);
}
-
- if (mouseDragging && (evt.getY() >= getHeight()) && (av
- .getAlignment().getHeight() > av.getRanges().getEndSeq()))
+ else if (mousePos.y >= getHeight())
{
- av.getRanges().scrollUp(false);
+ // mouse is below this panel - try scroll down
+ scrolled = ranges.scrollUp(false);
}
- if (mouseDragging && (evt.getX() < 0))
+ /*
+ * scroll left or right
+ */
+ if (mousePos.x < 0)
{
- av.getRanges().scrollRight(false);
+ scrolled |= ranges.scrollRight(false);
}
- else if (mouseDragging && (evt.getX() >= getWidth()))
+ else if (mousePos.x >= getWidth())
{
- av.getRanges().scrollRight(true);
+ scrolled |= ranges.scrollRight(true);
+ }
+ if (!scrolled)
+ {
+ /*
+ * we have reached the limit of the visible alignment - quit
+ */
+ threadRunning = false;
+ SeqPanel.this.ap.repaint();
}
}
import jalview.renderer.ResidueShaderI;
import jalview.util.MessageManager;
+import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
public void setAllGroupsCheckEnabled(boolean b)
{
allGroupsCheck.setEnabled(b);
- allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
}
/**
}
return title;
}
+
+ @Override
+ protected void allGroupsCheck_actionPerformed(ActionEvent e)
+ {
+ if (allGroupsCheck.isSelected())
+ {
+ valueChanged(slider.getValue());
+ }
+ }
}
package jalview.jbgui;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenu showTranslation = new JMenu();
protected JMenuItem showReverse = new JMenuItem();
vamsasStore_actionPerformed(e);
}
});
- showTranslation
- .setText(MessageManager.getString("label.translate_cDNA"));
- showTranslation.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
+
+ /*
+ * Translate as cDNA with sub-menu of translation tables
+ */
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
+ boolean first = true;
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
+ {
+ JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+ showTranslation.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(table);
+ }
+ });
+ if (first)
{
- showTranslation_actionPerformed(e);
+ showTranslation.addSeparator();
}
- });
+ first = false;
+ }
+
showReverse.setText(MessageManager.getString("label.reverse"));
showReverse.addActionListener(new ActionListener()
{
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.jbgui;
-
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JEditorPane;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.JTextField;
-import javax.swing.SwingConstants;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
-
-public class GDasSourceBrowser extends JPanel
-{
- public GDasSourceBrowser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- this.setLayout(gridBagLayout1);
- refresh.setText(
- MessageManager.getString("label.refresh_available_sources"));
- refresh.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- refresh_actionPerformed(e);
- }
- });
- progressBar.setPreferredSize(new Dimension(450, 20));
- progressBar.setString("");
- scrollPane.setBorder(titledBorder1);
- scrollPane.setBorder(BorderFactory.createEtchedBorder());
- fullDetailsScrollpane.setBorder(BorderFactory.createEtchedBorder());
- fullDetails.addHyperlinkListener(new HyperlinkListener()
- {
- public void hyperlinkUpdate(HyperlinkEvent e)
- {
- fullDetails_hyperlinkUpdate(e);
- }
- });
- fullDetails.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- fullDetails.setEditable(false);
- registryLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- registryLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- registryLabel.setText(MessageManager.getString("label.use_registry"));
- addLocal.setText(MessageManager.getString("label.add_local_source"));
- addLocal.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- amendLocal(true);
- }
- });
- jPanel1.setLayout(flowLayout1);
- jPanel1.setMinimumSize(new Dimension(596, 30));
- jPanel1.setPreferredSize(new Dimension(596, 30));
- jScrollPane2.setBorder(titledBorder3);
- jScrollPane3.setBorder(titledBorder4);
- jScrollPane4.setBorder(titledBorder5);
- titledBorder2
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- titledBorder3
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- titledBorder4
- .setTitleFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter1.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter2.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- filter3.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- table.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- reset.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- reset.setMargin(new Insets(2, 2, 2, 2));
- reset.setText(MessageManager.getString("action.reset"));
- reset.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- reset_actionPerformed(e);
- }
- });
- jPanel2.setLayout(borderLayout1);
- borderLayout1.setHgap(5);
- registryURL.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- scrollPane.getViewport().add(table);
- fullDetailsScrollpane.getViewport().add(fullDetails);
- jScrollPane3.getViewport().add(filter2);
- jScrollPane4.getViewport().add(filter3);
- jPanel1.add(refresh, null);
- jPanel1.add(addLocal, null);
- jPanel1.add(progressBar, null);
- jScrollPane2.getViewport().add(filter1);
- this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
- new Insets(0, 0, 0, 0), 0, 0));
- this.add(fullDetailsScrollpane,
- new GridBagConstraints(1, 0, 2, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(3, 0, 0, 3), 240, 130));
- this.add(scrollPane,
- new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(3, 2, 0, 0), 150, 130));
- jPanel2.add(registryLabel, java.awt.BorderLayout.WEST);
- jPanel2.add(registryURL, java.awt.BorderLayout.CENTER);
- jPanel2.add(reset, java.awt.BorderLayout.EAST);
- this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0,
- GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
- new Insets(5, 10, 0, 10), 339, 0));
- this.add(jScrollPane2,
- new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, 0, 0, 60), 80, 60));
- this.add(jScrollPane4,
- new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, -80, 0, 0), 80, 60));
- this.add(jScrollPane3,
- new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(0, -60, 0, 80), 80, 60));
- }
-
- protected JTable table = new JTable();
-
- protected JEditorPane fullDetails = new JEditorPane("text/html", "");
-
- TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.available_das_sources"));
-
- protected JButton refresh = new JButton();
-
- protected JProgressBar progressBar = new JProgressBar();
-
- protected JScrollPane scrollPane = new JScrollPane();
-
- TitledBorder titledBorder2 = new TitledBorder(
- MessageManager.getString("label.full_details"));
-
- protected JScrollPane fullDetailsScrollpane = new JScrollPane();
-
- protected JList filter1 = new JList();
-
- protected JList filter2 = new JList();
-
- protected JList filter3 = new JList();
-
- JScrollPane jScrollPane2 = new JScrollPane();
-
- JScrollPane jScrollPane3 = new JScrollPane();
-
- JScrollPane jScrollPane4 = new JScrollPane();
-
- protected JTextField registryURL = new JTextField();
-
- protected JLabel registryLabel = new JLabel();
-
- protected JButton addLocal = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- GridBagLayout gridBagLayout1 = new GridBagLayout();
-
- TitledBorder titledBorder3 = new TitledBorder(
- MessageManager.getString("label.authority") + ":");
-
- TitledBorder titledBorder4 = new TitledBorder(
- MessageManager.getString("label.type") + ":");
-
- TitledBorder titledBorder5 = new TitledBorder(
- MessageManager.getString("label.label") + ":");
-
- JButton reset = new JButton();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- public void refresh_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void fullDetails_hyperlinkUpdate(HyperlinkEvent e)
- {
- try
- {
-
- if (e.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
- {
- jalview.util.BrowserLauncher.openURL(e.getURL().toString());
- }
- } catch (Exception ex)
- {
- System.out.println(e.getURL());
- ex.printStackTrace();
- }
- }
-
- public void amendLocal(boolean newSource)
- {
-
- }
-
- public void reset_actionPerformed(ActionEvent e)
- {
-
- }
-
-}
public class GFinder extends JPanel
{
- JLabel jLabelFind = new JLabel();
+ private static final java.awt.Font VERDANA_12 = new java.awt.Font("Verdana", 0,
+ 12);
- protected JButton findAll = new JButton();
-
- protected JButton findNext = new JButton();
-
- JPanel actionsPanel = new JPanel();
-
- GridLayout gridLayout1 = new GridLayout();
+ private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
protected JButton createFeatures = new JButton();
- protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+ protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
getCacheKey());
- BorderLayout mainBorderLayout = new BorderLayout();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- JPanel jPanel4 = new JPanel();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- JPanel jPanel6 = new JPanel();
-
protected JCheckBox caseSensitive = new JCheckBox();
protected JCheckBox searchDescription = new JCheckBox();
- GridLayout optionsGridLayout = new GridLayout();
-
- private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
-
public GFinder()
{
try
private void jbInit() throws Exception
{
- jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabelFind.setText(MessageManager.getString("label.find"));
+ BorderLayout mainBorderLayout = new BorderLayout();
this.setLayout(mainBorderLayout);
- findAll.setFont(new java.awt.Font("Verdana", 0, 12));
- findAll.setText(MessageManager.getString("action.find_all"));
+ mainBorderLayout.setHgap(5);
+ mainBorderLayout.setVgap(5);
+
+ JLabel jLabelFind = new JLabel(MessageManager.getString("label.find"));
+ jLabelFind.setFont(VERDANA_12);
+
+ JButton findAll = new JButton(
+ MessageManager.getString("action.find_all"));
+ findAll.setFont(VERDANA_12);
findAll.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- findAll_actionPerformed(e);
+ findAll_actionPerformed();
}
});
- findNext.setFont(new java.awt.Font("Verdana", 0, 12));
- findNext.setText(MessageManager.getString("action.find_next"));
+
+ JButton findNext = new JButton(
+ MessageManager.getString("action.find_next"));
+ findNext.setFont(VERDANA_12);
findNext.addActionListener(new java.awt.event.ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- findNext_actionPerformed(e);
+ findNext_actionPerformed();
}
});
+
+ JPanel actionsPanel = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
actionsPanel.setLayout(gridLayout1);
gridLayout1.setHgap(0);
gridLayout1.setRows(3);
gridLayout1.setVgap(2);
+
createFeatures.setEnabled(false);
- createFeatures.setFont(new java.awt.Font("Verdana", 0, 12));
+ createFeatures.setFont(VERDANA_12);
createFeatures.setMargin(new Insets(0, 0, 0, 0));
createFeatures.setText(MessageManager.getString("label.new_feature"));
createFeatures.addActionListener(new java.awt.event.ActionListener()
@Override
public void caretUpdate(CaretEvent e)
{
- textfield_caretUpdate(e);
+ textfield_caretUpdate();
}
});
searchBox.getEditor().getEditorComponent()
textfield_keyPressed(e);
}
});
- mainBorderLayout.setHgap(5);
- mainBorderLayout.setVgap(5);
- jPanel4.setLayout(borderLayout2);
- jPanel2.setPreferredSize(new Dimension(10, 1));
- jPanel3.setPreferredSize(new Dimension(10, 1));
+
caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
caseSensitive.setText(MessageManager.getString("label.match_case"));
actionsPanel.add(createFeatures, null);
this.add(jLabelFind, java.awt.BorderLayout.WEST);
this.add(actionsPanel, java.awt.BorderLayout.EAST);
+
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setPreferredSize(new Dimension(10, 1));
+ JPanel jPanel3 = new JPanel();
+ jPanel3.setPreferredSize(new Dimension(10, 1));
+ JPanel jPanel4 = new JPanel();
+ jPanel4.setLayout(new BorderLayout());
this.add(jPanel2, java.awt.BorderLayout.SOUTH);
this.add(jPanel3, java.awt.BorderLayout.NORTH);
this.add(jPanel4, java.awt.BorderLayout.CENTER);
JPanel optionsPanel = new JPanel();
+ GridLayout optionsGridLayout = new GridLayout();
optionsGridLayout.setHgap(0);
optionsGridLayout.setRows(2);
optionsGridLayout.setVgap(2);
if (!searchBox.isPopupVisible())
{
e.consume();
- findNext_actionPerformed(null);
+ findNext_actionPerformed();
}
}
}
- protected void findNext_actionPerformed(ActionEvent e)
+ protected void findNext_actionPerformed()
{
}
- protected void findAll_actionPerformed(ActionEvent e)
+ protected void findAll_actionPerformed()
{
}
{
}
- public void textfield_caretUpdate(CaretEvent e)
+ public void textfield_caretUpdate()
{
- if (searchBox.getUserInput().indexOf(">") > -1)
+ // disabled as appears to be running a non-functional
+ if (false && searchBox.getUserInput().indexOf(">") > -1)
{
SwingUtilities.invokeLater(new Runnable()
{
str = jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars,
al.getSequenceAt(0).getSequenceAsString());
-
+ // todo and what? set str as searchBox text?
}
}
});
setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
backupfilesConfirmDelete.setLabels(
- MessageManager.getString("label.confirm_delete"),
+ MessageManager.getString("label.always_ask"),
MessageManager.getString("label.auto_delete"));
// update the enabled section
keepRollMaxOptionsEnabled();
return this;
}
-}
\ No newline at end of file
+}
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();
}
else
{
- seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ seqannot = new IdentityHashMap<>();
}
// resolve the context containing all the annotation for the sequence
AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
&& value >= ann.threshold.value)
{
- range = (value - ann.threshold.value)
+ range = ann.graphMax == ann.threshold.value ? 1f
+ : (value - ann.threshold.value)
/ (ann.graphMax - ann.threshold.value);
}
else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
&& value <= ann.threshold.value)
{
- range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+ range = ann.graphMin == ann.threshold.value ? 0f
+ : (value - ann.graphMin)
+ / (ann.threshold.value - ann.graphMin);
}
else
{
import jalview.datamodel.features.FeatureMatcher;
import jalview.util.ColorUtils;
import jalview.util.Format;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.util.StringTokenizer;
*/
public class FeatureColour implements FeatureColourI
{
+ private static final String I18N_LABEL = MessageManager
+ .getString("label.label");
+
+ private static final String I18N_SCORE = MessageManager
+ .getString("label.score");
+
private static final String ABSOLUTE = "abso";
private static final String ABOVE = "above";
Color maxColour = ColorUtils.parseColourString(maxcol);
Color noColour = noValueColour.equals(NO_VALUE_MAX) ? maxColour
: (noValueColour.equals(NO_VALUE_NONE) ? null : minColour);
- featureColour = new FeatureColour(minColour, maxColour, noColour, min,
- max);
+ featureColour = new FeatureColour(maxColour, minColour, maxColour,
+ noColour, min, max);
featureColour.setColourByLabel(minColour == null);
featureColour.setAutoScaled(autoScaled);
if (byAttribute)
}
/**
- * Constructor given a simple colour
+ * Constructor given a simple colour. This also 'primes' a graduated colour
+ * range, where the maximum colour is the given simple colour, and the minimum
+ * colour a paler shade of it. This is for convenience when switching from a
+ * simple colour to a graduated colour scheme.
*
* @param c
*/
public FeatureColour(Color c)
{
- minColour = Color.WHITE;
- maxColour = Color.BLACK;
- noColour = DEFAULT_NO_COLOUR;
- minRed = 0f;
- minGreen = 0f;
- minBlue = 0f;
- deltaRed = 0f;
- deltaGreen = 0f;
- deltaBlue = 0f;
- colour = c;
- }
+ /*
+ * set max colour to the simple colour, min colour to a paler shade of it
+ */
+ this(c, c == null ? Color.white : ColorUtils.bleachColour(c, 0.9f),
+ c == null ? Color.black : c, DEFAULT_NO_COLOUR, 0, 0);
- /**
- * Constructor given a colour range and a score range, defaulting 'no value
- * colour' to be the same as minimum colour
- *
- * @param low
- * @param high
- * @param min
- * @param max
- */
- public FeatureColour(Color low, Color high, float min, float max)
- {
- this(low, high, low, min, max);
+ /*
+ * but enforce simple colour for now!
+ */
+ setGraduatedColour(false);
}
/**
}
/**
- * Copy constructor with new min/max ranges
- *
- * @param fc
- * @param min
- * @param max
- */
- public FeatureColour(FeatureColour fc, float min, float max)
- {
- this(fc);
- updateBounds(min, max);
- }
-
- /**
- * Constructor for a graduated colour
+ * Constructor that sets both simple and graduated colour values. This allows
+ * alternative colour schemes to be 'preserved' while switching between them
+ * to explore their effects on the visualisation.
+ * <p>
+ * This sets the colour scheme to 'graduated' by default. Override this if
+ * wanted by calling <code>setGraduatedColour(false)</code> for a simple
+ * colour, or <code>setColourByLabel(true)</code> for colour by label.
*
+ * @param myColour
* @param low
* @param high
* @param noValueColour
* @param min
* @param max
*/
- public FeatureColour(Color low, Color high, Color noValueColour,
- float min, float max)
+ public FeatureColour(Color myColour, Color low, Color high,
+ Color noValueColour, float min, float max)
{
if (low == null)
{
{
high = Color.black;
}
- graduatedColour = true;
- colour = null;
+ colour = myColour;
minColour = low;
maxColour = high;
+ setGraduatedColour(true);
noColour = noValueColour;
threshold = Float.NaN;
isHighToLow = min >= max;
* Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
* false.
*/
- void setGraduatedColour(boolean b)
+ public void setGraduatedColour(boolean b)
{
graduatedColour = b;
if (b)
sb.append(BAR).append(Format.getHexString(getMinColour()))
.append(BAR);
sb.append(Format.getHexString(getMaxColour())).append(BAR);
- String noValue = minColour.equals(noColour) ? NO_VALUE_MIN
- : (maxColour.equals(noColour) ? NO_VALUE_MAX
- : NO_VALUE_NONE);
+
+ /*
+ * 'no value' colour should be null, min or max colour;
+ * if none of these, coerce to minColour
+ */
+ String noValue = NO_VALUE_MIN;
+ if (maxColour.equals(noColour))
+ {
+ noValue = NO_VALUE_MAX;
+ }
+ if (noColour == null)
+ {
+ noValue = NO_VALUE_NONE;
+ }
sb.append(noValue).append(BAR);
if (!isAutoScaled())
{
|| (isBelowThreshold() && scr >= threshold));
}
+ @Override
+ public String getDescription()
+ {
+ if (isSimpleColour())
+ {
+ return "r=" + colour.getRed() + ",g=" + colour.getGreen() + ",b="
+ + colour.getBlue();
+ }
+ StringBuilder tt = new StringBuilder();
+ String by = null;
+
+ if (getAttributeName() != null)
+ {
+ by = FeatureMatcher.toAttributeDisplayName(getAttributeName());
+ }
+ else if (isColourByLabel())
+ {
+ by = I18N_LABEL;
+ }
+ else
+ {
+ by = I18N_SCORE;
+ }
+ tt.append(MessageManager.formatMessage("action.by_title_param", by));
+
+ /*
+ * add threshold if any
+ */
+ if (isAboveThreshold() || isBelowThreshold())
+ {
+ tt.append(" (");
+ if (isColourByLabel())
+ {
+ /*
+ * Jalview features file supports the combination of
+ * colour by label or attribute text with score threshold
+ */
+ tt.append(I18N_SCORE).append(" ");
+ }
+ tt.append(isAboveThreshold() ? "> " : "< ");
+ tt.append(getThreshold()).append(")");
+ }
+
+ return tt.toString();
+ }
+
}
*/
package jalview.schemes;
+import jalview.analysis.GeneticCodes;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
public static String START = "ATG";
- /**
- * Nucleotide Ambiguity Codes
- */
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
-
- /**
- * Codon triplets with additional symbols for unambiguous codons that include
- * ambiguity codes
- */
- public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
-
- /**
- * all ambiguity codes for a given base
- */
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
-
- static
- {
- /*
- * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
- */
- ambiguityCodes.put("R", new String[] { "A", "G" });
- ambiguityCodes.put("Y", new String[] { "T", "C" });
- ambiguityCodes.put("W", new String[] { "A", "T" });
- ambiguityCodes.put("S", new String[] { "G", "C" });
- ambiguityCodes.put("M", new String[] { "A", "C" });
- ambiguityCodes.put("K", new String[] { "G", "T" });
- ambiguityCodes.put("H", new String[] { "A", "T", "C" });
- ambiguityCodes.put("B", new String[] { "G", "T", "C" });
- ambiguityCodes.put("V", new String[] { "G", "A", "C" });
- ambiguityCodes.put("D", new String[] { "G", "A", "T" });
- ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" });
-
- // Now build codon translation table
- codonHash2.put("AAA", "K");
- codonHash2.put("AAG", "K");
- codonHash2.put("AAC", "N");
- codonHash2.put("AAT", "N");
-
- codonHash2.put("CAA", "Q");
- codonHash2.put("CAG", "Q");
- codonHash2.put("CAC", "H");
- codonHash2.put("CAT", "H");
-
- codonHash2.put("GAA", "E");
- codonHash2.put("GAG", "E");
- codonHash2.put("GAC", "D");
- codonHash2.put("GAT", "D");
-
- codonHash2.put("TAC", "Y");
- codonHash2.put("TAT", "Y");
-
- codonHash2.put("ACA", "T");
- codonHash2.put("ACC", "T");
- codonHash2.put("ACT", "T");
- codonHash2.put("ACG", "T");
-
- codonHash2.put("CCA", "P");
- codonHash2.put("CCG", "P");
- codonHash2.put("CCC", "P");
- codonHash2.put("CCT", "P");
-
- codonHash2.put("GCA", "A");
- codonHash2.put("GCG", "A");
- codonHash2.put("GCC", "A");
- codonHash2.put("GCT", "A");
-
- codonHash2.put("TCA", "S");
- codonHash2.put("TCG", "S");
- codonHash2.put("TCC", "S");
- codonHash2.put("TCT", "S");
- codonHash2.put("AGC", "S");
- codonHash2.put("AGT", "S");
-
- codonHash2.put("AGA", "R");
- codonHash2.put("AGG", "R");
- codonHash2.put("CGA", "R");
- codonHash2.put("CGG", "R");
- codonHash2.put("CGC", "R");
- codonHash2.put("CGT", "R");
-
- codonHash2.put("GGA", "G");
- codonHash2.put("GGG", "G");
- codonHash2.put("GGC", "G");
- codonHash2.put("GGT", "G");
-
- codonHash2.put("TGA", "*");
- codonHash2.put("TAA", "*");
- codonHash2.put("TAG", "*");
-
- codonHash2.put("TGG", "W");
-
- codonHash2.put("TGC", "C");
- codonHash2.put("TGT", "C");
-
- codonHash2.put("ATA", "I");
- codonHash2.put("ATC", "I");
- codonHash2.put("ATT", "I");
-
- codonHash2.put("ATG", "M");
-
- codonHash2.put("CTA", "L");
- codonHash2.put("CTG", "L");
- codonHash2.put("CTC", "L");
- codonHash2.put("CTT", "L");
- codonHash2.put("TTA", "L");
- codonHash2.put("TTG", "L");
-
- codonHash2.put("GTA", "V");
- codonHash2.put("GTG", "V");
- codonHash2.put("GTC", "V");
- codonHash2.put("GTT", "V");
-
- codonHash2.put("TTC", "F");
- codonHash2.put("TTT", "F");
-
- buildAmbiguityCodonSet();
- }
-
- /**
- * programmatic generation of codons including ambiguity codes
- */
- public static void buildAmbiguityCodonSet()
- {
- if (_ambiguityCodes.size() > 0)
- {
- System.err
- .println("Ignoring multiple calls to buildAmbiguityCodonSet");
- return;
- }
- // Invert the ambiguity code set
- for (Map.Entry<String, String[]> acode : ambiguityCodes.entrySet())
- {
- for (String r : acode.getValue())
- {
- List<String> codesfor = _ambiguityCodes.get(r);
- if (codesfor == null)
- {
- _ambiguityCodes.put(r, codesfor = new ArrayList<>());
- }
- if (!codesfor.contains(acode.getKey()))
- {
- codesfor.add(acode.getKey());
- }
- else
- {
- System.err.println(
- "Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
- + acode.getKey() + " in residue " + r);
- }
- }
- }
- // and programmatically add in the ambiguity codes that yield the same amino
- // acid
- String[] unambcodons = codonHash2.keySet()
- .toArray(new String[codonHash2.size()]);
- for (String codon : unambcodons)
- {
- String residue = codonHash2.get(codon);
- String acodon[][] = new String[codon.length()][];
- for (int i = 0, iSize = codon.length(); i < iSize; i++)
- {
- String _ac = "" + codon.charAt(i);
- List<String> acodes = _ambiguityCodes.get(_ac);
- if (acodes != null)
- {
- acodon[i] = acodes.toArray(new String[acodes.size()]);
- }
- else
- {
- acodon[i] = new String[] {};
- }
- }
- // enumerate all combinations and test for veracity of translation
- int tpos[] = new int[codon.length()],
- cpos[] = new int[codon.length()];
- for (int i = 0; i < tpos.length; i++)
- {
- tpos[i] = -1;
- }
- tpos[acodon.length - 1] = 0;
- int ipos, j;
- while (tpos[0] < acodon[0].length)
- {
- // make all codons for this combination
- char allres[][] = new char[tpos.length][];
- String _acodon = "";
- for (ipos = 0; ipos < tpos.length; ipos++)
- {
- if (acodon[ipos].length == 0 || tpos[ipos] < 0)
- {
- _acodon += codon.charAt(ipos);
- allres[ipos] = new char[] { codon.charAt(ipos) };
- }
- else
- {
- _acodon += acodon[ipos][tpos[ipos]];
- String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]);
- allres[ipos] = new char[altbase.length];
- j = 0;
- for (String ab : altbase)
- {
- allres[ipos][j++] = ab.charAt(0);
- }
- }
- }
- // test all codons for this combination
- for (ipos = 0; ipos < cpos.length; ipos++)
- {
- cpos[ipos] = 0;
- }
- boolean valid = true;
- do
- {
- String _codon = "";
- for (j = 0; j < cpos.length; j++)
- {
- _codon += allres[j][cpos[j]];
- }
- String tr = codonHash2.get(_codon);
- if (valid = (tr != null && tr.equals(residue)))
- {
- // advance to next combination
- ipos = acodon.length - 1;
- while (++cpos[ipos] >= allres[ipos].length && ipos > 0)
- {
- cpos[ipos] = 0;
- ipos--;
- }
- }
- } while (valid && cpos[0] < allres[0].length);
- if (valid)
- {
- // Add this to the set of codons we will translate
- // System.out.println("Adding ambiguity codon: " + _acodon + " for "
- // + residue);
- codonHash2.put(_acodon, residue);
- }
- else
- {
- // System.err.println("Rejecting ambiguity codon: " + _acodon
- // + " for " + residue);
- }
- // next combination
- ipos = acodon.length - 1;
- while (++tpos[ipos] >= acodon[ipos].length && ipos > 0)
- {
- tpos[ipos] = -1;
- ipos--;
- }
- }
- }
- }
-
// Stores residue codes/names and colours and other things
public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
public static String codonTranslate(String lccodon)
{
- String cdn = codonHash2.get(lccodon.toUpperCase());
- if ("*".equals(cdn))
+ String peptide = GeneticCodes.getInstance().getStandardCodeTable()
+ .translate(lccodon);
+ if ("*".equals(peptide))
{
- return STOP;
+ return "STOP";
}
- return cdn;
+ return peptide;
}
/*
/*
* lookup from lower-case form of a name to its canonical (standardised) form
*/
- private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
+ private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- private static Map<String, String> dasCoordinateSystemsLookup = new HashMap<String, String>();
static
{
canonicalSourceNameLookup.get(k));
}
- dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
- dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
- dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBL);
- // dasCoordinateSystemsLookup.put("embl", DBRefSource.EMBLCDS);
}
/**
{
return dbrefs;
}
- HashSet<String> srcs = new HashSet<String>();
+ HashSet<String> srcs = new HashSet<>();
for (String src : sources)
{
srcs.add(src.toUpperCase());
}
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> res = new ArrayList<>();
for (DBRefEntry dbr : dbrefs)
{
String source = getCanonicalName(dbr.getSource());
}
/**
- * isDasCoordinateSystem
- *
- * @param string
- * String
- * @param dBRefEntry
- * DBRefEntry
- * @return boolean true if Source DBRefEntry is compatible with DAS
- * CoordinateSystem name
- */
-
- public static boolean isDasCoordinateSystem(String string,
- DBRefEntry dBRefEntry)
- {
- if (string == null || dBRefEntry == null)
- {
- return false;
- }
- String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
- return coordsys == null ? false
- : coordsys.equals(dBRefEntry.getSource());
- }
-
- /**
* look up source in an internal list of database reference sources and return
* the canonical jalview name for the source, or the original string if it has
* no canonical form.
static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
DbRefComp comparator)
{
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || entry == null)
{
return rfs;
public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
String source)
{
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> matches = new ArrayList<>();
if (dbRefs != null && source != null)
{
for (DBRefEntry dbref : dbRefs)
// nothing to do
return;
}
- List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> selfs = new ArrayList<>();
{
DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
sequence.getDBRefs());
selfs.remove(p);
}
}
- List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> toPromote = new ArrayList<>();
for (DBRefEntry p : pr)
{
- List<String> promType = new ArrayList<String>();
+ List<String> promType = new ArrayList<>();
if (sequence.isProtein())
{
switch (getCanonicalName(p.getSource()))
*/
public int getVisibleAlignmentWidth()
{
- return al.getWidth() - al.getHiddenColumns().getSize();
+ return al.getVisibleWidth();
}
/**
protected void eraseConsensus(int aWidth)
{
AlignmentAnnotation consensus = getConsensusAnnotation();
- consensus.annotations = new Annotation[aWidth];
+ if (consensus != null)
+ {
+ consensus.annotations = new Annotation[aWidth];
+ }
AlignmentAnnotation gap = getGapAnnotation();
if (gap != null)
{
// and remove it from the rest
// TODO: decide if we should remove annotated sequence from set
sdataset.remove(sequence);
- // TODO: should we make a note of sequences that have received new DB
- // ids, so we can query all enabled DAS servers for them ?
}
}
return modified;
{
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
- FeatureColourI ggc = new FeatureColour(Color.white,
- gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
+ FeatureColourI ggc = new FeatureColour(gc.getColour(),
+ Color.white, gc.getColour(), Color.white,
+ Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}
assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+ assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
}
@Test(groups = { "Functional" })
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
alf.getWidth(), false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna();
+ AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
assertTrue("Translation failed (ipos=" + ipos
+ ") No alignment data.", transAlf != null);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
}
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna();
+ AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna();
+ AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
+ .getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import java.util.List;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class FinderTest
{
@BeforeClass(alwaysRun = true)
private AlignmentI al;
+ private AlignViewportI av;
+
@BeforeClass(groups = "Functional")
public void setUp()
{
- String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.FALSE.toString());
+
+ String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
+ "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
- al = af.getViewport().getAlignment();
+ av = af.getViewport();
+ al = av.getAlignment();
+ }
+
+ @AfterMethod
+ public void tearDownAfterTest()
+ {
+ av.setSelectionGroup(null);
}
/**
- * Test for find all matches of a regular expression
+ * Test for find matches of a regular expression
*/
@Test(groups = "Functional")
- public void testFindAll_regex()
+ public void testFind_regex()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("E.H"); // 'E, any character, H'
+ /*
+ * find next match only
+ */
+ Finder f = new Finder(av);
+ f.findNext("E.H", false, false); // 'E, any character, H'
+ // should match seq2 efH only
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 1);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ f = new Finder(av);
+ f.findAll("E.H", false, false); // 'E, any character, H'
// should match seq2 efH and seq3 EFH
- SearchResultsI sr = f.getSearchResults();
+ sr = f.getSearchResults();
assertEquals(sr.getSize(), 2);
- List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
assertEquals(matches.get(0).getStart(), 5);
assertEquals(matches.get(0).getEnd(), 7);
assertEquals(matches.get(1).getStart(), 4);
@Test(groups = "Functional")
public void testFind_residueNumber()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("9");
+ Finder f = new Finder(av);
- // seq1 and seq4 have 9 residues; no match in other sequences
+ /*
+ * find first match should return seq1 residue 9
+ */
+ f.findNext("9", false, false);
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getSize(), 2);
+ assertEquals(sr.getSize(), 1);
List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+
+ /*
+ * find all matches should return seq1 and seq4 (others are too short)
+ */
+ f = new Finder(av);
+ f.findAll("9", false, false);
+ sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
assertEquals(matches.get(0).getStart(), 9);
assertEquals(matches.get(0).getEnd(), 9);
assertEquals(matches.get(1).getStart(), 9);
assertEquals(matches.get(1).getEnd(), 9);
+
+ /*
+ * parsing of search string as integer is strict
+ */
+ f = new Finder(av);
+ f.findNext(" 9", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
}
/**
public void testFindNext()
{
/*
- * start at second sequence; resIndex of -1
+ * start at second sequence; colIndex of -1
* means sequence id / description is searched
*/
- Finder f = new Finder(al, null, 1, -1);
- f.find("e"); // matches id
+ Finder f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", -1);
+ f.findNext("e", false, false); // matches id
assertTrue(f.getSearchResults().isEmpty());
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
-
- // resIndex is now 0 - for use in next find next
- assertEquals(f.getResIndex(), 0);
- f = new Finder(al, null, 1, 0);
- f.find("e"); // matches in sequence
- assertTrue(f.getIdMatch().isEmpty());
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+
+ // colIndex is now 0 - for use in next find next
+ // searching A--BCDefHI
+ assertEquals(PA.getValue(f, "columnIndex"), 0);
+ f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", 0);
+ f.findNext("e", false, false); // matches in sequence
+ assertTrue(f.getIdMatches().isEmpty());
assertEquals(f.getSearchResults().getSize(), 1);
List<SearchResultMatchI> matches = f.getSearchResults().getResults();
assertEquals(matches.get(0).getStart(), 5);
assertEquals(matches.get(0).getEnd(), 5);
assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
// still in the second sequence
- assertEquals(f.getSeqIndex(), 1);
- // next residue position to search from is 5
- // (used as base 0 by RegEx so the same as 6 if base 1)
- assertEquals(f.getResIndex(), 5);
+ assertEquals(PA.getValue(f, "sequenceIndex"), 1);
+ // next column position to search from is 7
+ assertEquals(PA.getValue(f, "columnIndex"), 7);
// find next from end of sequence - finds next sequence id
- f = new Finder(al, null, 1, 5);
- f.find("e");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
+ f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "columnIndex", 7);
+ f.findNext("e", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
+ assertTrue(f.getSearchResults().isEmpty());
}
/**
* Test for matching within sequence descriptions
*/
@Test(groups = "Functional")
- public void testFindAll_inDescription()
+ public void testFind_inDescription()
{
AlignmentI al2 = new Alignment(al);
al2.getSequenceAt(0).setDescription("BRAF");
al2.getSequenceAt(1).setDescription("braf");
- Finder f = new Finder(al2, null);
- f.setFindAll(true);
- f.setIncludeDescription(true);
-
- f.find("rAF");
- assertEquals(f.getIdMatch().size(), 2);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
- assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+
+ AlignViewportI av2 = new AlignViewport(al2);
+
+ /*
+ * find first match only
+ */
+ Finder f = new Finder(av2);
+ f.findNext("rAF", false, true);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
/*
- * case sensitive
+ * find all matches
*/
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.setIncludeDescription(true);
+ f = new Finder(av2);
+ f.findAll("rAF", false, true);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
+ assertTrue(f.getSearchResults().isEmpty());
- f.find("RAF");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ /*
+ * case sensitive
+ */
+ f = new Finder(av2);
+ f.findAll("RAF", true, true);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
/*
al2.getSequenceAt(0).setDescription("the efh sequence");
al2.getSequenceAt(0).setName("mouseEFHkinase");
al2.getSequenceAt(1).setName("humanEFHkinase");
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.setIncludeDescription(true);
+ f = new Finder(av2);
/*
* sequence matches should have no duplicates
*/
- f.find("EFH");
- assertEquals(f.getIdMatch().size(), 2);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
- assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+ f.findAll("EFH", false, true);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+ assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
assertEquals(f.getSearchResults().getSize(), 2);
SearchResultMatchI match = f.getSearchResults().getResults().get(0);
- assertSame(al2.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
}
/**
@Test(groups = "Functional")
public void testFindAll_sequenceIds()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ Finder f = new Finder(av);
/*
- * case insensitive
+ * case insensitive; seq1 occurs twice in sequence id but
+ * only one match should be returned
*/
- f.find("SEQ1");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
- assertTrue(f.getSearchResults().isEmpty());
+ f.findAll("SEQ1", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
+ SearchResultsI searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
/*
* case sensitive
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("SEQ1");
- assertTrue(f.getSearchResults().isEmpty());
+ f = new Finder(av);
+ f.findAll("SEQ1", true, false);
+ searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
/*
* match both sequence id and sequence
*/
AlignmentI al2 = new Alignment(al);
+ AlignViewportI av2 = new AlignViewport(al2);
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.find("ABZ");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4));
- assertEquals(f.getSearchResults().getSize(), 2);
- SearchResultMatchI match = f.getSearchResults().getResults().get(0);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
- match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(10, match.getStart());
- assertEquals(12, match.getEnd());
+ f = new Finder(av2);
+ f.findAll("ABZ", false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 10);
+ assertEquals(match.getEnd(), 12);
}
/**
- * Test finding all matches of a sequence pattern in an alignment
+ * Test finding next match of a sequence pattern in an alignment
*/
@Test(groups = "Functional")
- public void testFindAll_simpleMatch()
+ public void testFind_findNext()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ /*
+ * efh should be matched in seq2 only
+ */
+ FinderI f = new Finder(av);
+ f.findNext("EfH", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
/*
- * case insensitive first
+ * I should be found in seq1 (twice) and seq2 (once)
*/
- f.find("EfH");
+ f = new Finder(av);
+ f.findNext("I", false, false); // find next: seq1/16
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+
+ f.findNext("I", false, false); // find next: seq1/18
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+
+ f.findNext("I", false, false); // find next: seq2/8
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+
+ f.findNext("I", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * find should reset to start of alignment after a failed search
+ */
+ f.findNext("I", false, false); // find next: seq1/16
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+ }
+
+ /**
+ * Test for JAL-2302 to verify that sub-matches are not included in a find all
+ * result
+ */
+ @Test(groups = "Functional")
+ public void testFind_maximalResultOnly()
+ {
+ Finder f = new Finder(av);
+ f.findAll("M+", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 4); // dataset sequence positions
+ assertEquals(match.getEnd(), 8); // base 1
+ }
+
+ /**
+ * Test finding all matches of a sequence pattern in an alignment
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAll()
+ {
+ Finder f = new Finder(av);
+ f.findAll("EfH", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
/*
- * case sensitive
+ * find all I should find 2 positions in seq1, 1 in seq2
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("BC");
+ f.findAll("I", false, false);
searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 3);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+ match = searchResults.getResults().get(2);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+ }
+
+ /**
+ * Test finding all matches, case-sensitive
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllCaseSensitive()
+ {
+ Finder f = new Finder(av);
+
+ /*
+ * BC should match seq1/9-10 and seq2/2-3
+ */
+ f.findAll("BC", true, false);
+ SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 10);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 3);
+
+ /*
+ * bc should match seq3/1-2
+ */
+ f = new Finder(av);
+ f.findAll("bc", true, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 2);
+
+ f.findAll("bC", true, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ }
+
+ /**
+ * Test finding next match of a sequence pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_inSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ av.setSelectionGroup(sg);
+
+ FinderI f = new Finder(av);
+ f.findNext("b", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 2);
+
+ /*
+ * a second Find should not return the 'b' in seq3 as outside the selection
+ */
+ f.findNext("b", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ assertTrue(f.getIdMatches().isEmpty());
+
+ f = new Finder(av);
+ f.findNext("d", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(0), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+ f.findNext("d", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 3);
+ assertEquals(match.getEnd(), 3);
+ }
+
+ /**
+ * Test finding all matches of a search pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * search for 'e' should match two sequence ids and one residue
+ */
+ Finder f = new Finder(av);
+ f.findAll("e", false, false);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+ assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * search for 'Q' should match two sequence ids only
+ */
+ f = new Finder(av);
+ f.findAll("Q", false, false);
+ assertEquals(f.getIdMatches().size(), 2);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+ assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
+ assertTrue(f.getSearchResults().isEmpty());
+ }
+
+ /**
+ * Test finding in selection with a sequence too short to reach it
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelectionWithShortSequence()
+ {
+ /*
+ * select all sequences, columns 10-12
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(9);
+ sg.setEndRes(11);
+ sg.addSequence(al.getSequenceAt(0), false);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ sg.addSequence(al.getSequenceAt(3), false);
+ av.setSelectionGroup(sg);
+
+ /*
+ * search for 'I' should match two sequence positions
+ */
+ Finder f = new Finder(av);
+ f.findAll("I", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
}
/**
- * Test for JAL-2302 to verify that sub-matches are not included in a find all
- * result
+ * Test that find does not report hidden positions
*/
@Test(groups = "Functional")
- public void testFind_maximalResultOnly()
+ public void testFind_withHiddenColumns()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("M+");
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+
+ /*
+ * hide 2-4 (CD- -BC bcd ---)
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ al.setHiddenColumns(hc);
+
+ /*
+ * find all search for D should ignore hidden positions in seq1 and seq3,
+ * find the visible D in seq2
+ */
+ Finder f = new Finder(av);
+ f.findAll("D", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(3), match.getSequence());
- assertEquals(4, match.getStart()); // dataset sequence positions
- assertEquals(8, match.getEnd()); // base 1
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * hide columns 2-5:
+ * find all 'aaa' should find end of seq4 only
+ */
+ hc.hideColumns(2, 5);
+ f = new Finder(av);
+ f.findAll("aaa", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 11);
+
+ /*
+ * find all 'BE' should not match across hidden columns in seq1
+ */
+ f.findAll("BE", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * boundary case: hide columns at end of alignment
+ * search for H should match seq3/6 only
+ */
+ hc.revealAllHiddenColumns(new ColumnSelection());
+ hc.hideColumns(8, 13);
+ f = new Finder(av);
+ f.findNext("H", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 6);
+ assertEquals(match.getEnd(), 6);
+ }
+
+ @Test(groups = "Functional")
+ public void testFind_withHiddenColumnsAndSelection()
+ {
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+
+ /*
+ * hide columns 2-4 and 6-7
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ hc.hideColumns(6, 7);
+ al.setHiddenColumns(hc);
+
+ /*
+ * select rows 2-3
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ sg.setStartRes(0);
+ sg.setEndRes(13);
+ av.setSelectionGroup(sg);
+
+ /*
+ * find all search for A or H
+ * should match seq2/1, seq2/7, not seq3/6
+ */
+ Finder f = new Finder(av);
+ f.findAll("[AH]", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 1);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 7);
+ assertEquals(match.getEnd(), 7);
}
}
--- /dev/null
+package jalview.analysis;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertSame;
+
+import java.util.Iterator;
+
+import org.testng.annotations.Test;
+
+public class GeneticCodesTest
+{
+ @Test(groups = "Functional")
+ public void testGetCodeTable()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+ assertEquals(codes.getStandardCodeTable().getName(), "Standard");
+ assertEquals(codes.getStandardCodeTable().getId(), "1");
+ assertSame(codes.getStandardCodeTable(), codes.getCodeTable("1"));
+ assertEquals(codes.getCodeTable("2").getName(),
+ "Vertebrate Mitochondrial");
+ assertEquals(codes.getCodeTable("11").getName(),
+ "Bacterial, Archaeal and Plant Plastid");
+ assertEquals(codes.getCodeTable("31").getName(),
+ "Blastocrithidia Nuclear");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetCodeTables()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+ Iterator<GeneticCodeI> tableIterator = codes.getCodeTables().iterator();
+ String[] ids = new String[] { "1", "2", "3", "4", "5", "6", "9", "10",
+ "11", "12", "13", "14", "15", "16", "21", "22", "23", "24", "25",
+ "26", "27", "28", "29", "30", "31" };
+ for (int i = 0; i < ids.length; i++)
+ {
+ assertEquals(tableIterator.next().getId(), ids[i]);
+ }
+ assertFalse(tableIterator.hasNext());
+ }
+
+ @Test(groups = "Functional")
+ public void testTranslate()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+
+ GeneticCodeI gc = codes.getCodeTable("1");
+ assertNull(gc.translate("XYZ"));
+ assertEquals(gc.translate("AGA"), "R");
+
+ gc = codes.getCodeTable("2");
+ assertEquals(gc.translate("AGA"), "*"); // variant
+ assertEquals(gc.translate("ttc"), "F"); // non-variant
+
+ // table 11 has no variant translations - should serve the standard values
+ gc = codes.getCodeTable("11");
+ assertEquals(gc.translate("ttc"), "F");
+
+ gc = codes.getCodeTable("31");
+ assertEquals(gc.translate("TGA"), "W"); // variant
+ assertEquals(gc.translate("tag"), "E"); // variant
+ assertEquals(gc.translate("AGC"), "S"); // non-variant
+ }
+
+ /**
+ * Test 'standard' codon translations (no ambiguity codes)
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_standardTable()
+ {
+ GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+ assertEquals("F", st.translate("TTT"));
+ assertEquals("F", st.translate("TTC"));
+ assertEquals("L", st.translate("TTA"));
+ assertEquals("L", st.translate("TTG"));
+ assertEquals("L", st.translate("CTT"));
+ assertEquals("L", st.translate("CTC"));
+ assertEquals("L", st.translate("CTA"));
+ assertEquals("L", st.translate("CTG"));
+ assertEquals("I", st.translate("ATT"));
+ assertEquals("I", st.translate("ATC"));
+ assertEquals("I", st.translate("ATA"));
+ assertEquals("M", st.translate("ATG"));
+ assertEquals("V", st.translate("GTT"));
+ assertEquals("V", st.translate("GTC"));
+ assertEquals("V", st.translate("GTA"));
+ assertEquals("V", st.translate("GTG"));
+ assertEquals("S", st.translate("TCT"));
+ assertEquals("S", st.translate("TCC"));
+ assertEquals("S", st.translate("TCA"));
+ assertEquals("S", st.translate("TCG"));
+ assertEquals("P", st.translate("CCT"));
+ assertEquals("P", st.translate("CCC"));
+ assertEquals("P", st.translate("CCA"));
+ assertEquals("P", st.translate("CCG"));
+ assertEquals("T", st.translate("ACT"));
+ assertEquals("T", st.translate("ACC"));
+ assertEquals("T", st.translate("ACA"));
+ assertEquals("T", st.translate("ACG"));
+ assertEquals("A", st.translate("GCT"));
+ assertEquals("A", st.translate("GCC"));
+ assertEquals("A", st.translate("GCA"));
+ assertEquals("A", st.translate("GCG"));
+ assertEquals("Y", st.translate("TAT"));
+ assertEquals("Y", st.translate("TAC"));
+ assertEquals("*", st.translate("TAA"));
+ assertEquals("*", st.translate("TAG"));
+ assertEquals("H", st.translate("CAT"));
+ assertEquals("H", st.translate("CAC"));
+ assertEquals("Q", st.translate("CAA"));
+ assertEquals("Q", st.translate("CAG"));
+ assertEquals("N", st.translate("AAT"));
+ assertEquals("N", st.translate("AAC"));
+ assertEquals("K", st.translate("AAA"));
+ assertEquals("K", st.translate("AAG"));
+ assertEquals("D", st.translate("GAT"));
+ assertEquals("D", st.translate("GAC"));
+ assertEquals("E", st.translate("GAA"));
+ assertEquals("E", st.translate("GAG"));
+ assertEquals("C", st.translate("TGT"));
+ assertEquals("C", st.translate("TGC"));
+ assertEquals("*", st.translate("TGA"));
+ assertEquals("W", st.translate("TGG"));
+ assertEquals("R", st.translate("CGT"));
+ assertEquals("R", st.translate("CGC"));
+ assertEquals("R", st.translate("CGA"));
+ assertEquals("R", st.translate("CGG"));
+ assertEquals("S", st.translate("AGT"));
+ assertEquals("S", st.translate("AGC"));
+ assertEquals("R", st.translate("AGA"));
+ assertEquals("R", st.translate("AGG"));
+ assertEquals("G", st.translate("GGT"));
+ assertEquals("G", st.translate("GGC"));
+ assertEquals("G", st.translate("GGA"));
+ assertEquals("G", st.translate("GGG"));
+ }
+
+ /**
+ * Test a sample of codon translations involving ambiguity codes. Should
+ * return a protein value where the ambiguity does not affect the translation.
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_standardTableAmbiguityCodes()
+ {
+ GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+ // Y is C or T
+ assertEquals("C", st.translate("TGY"));
+ // Phenylalanine first base variation
+ assertEquals("L", st.translate("YTA"));
+
+ // W is A or T
+ assertEquals("L", st.translate("CTW"));
+ assertNull(st.translate("TTW"));
+
+ // S is G or C
+ assertEquals("G", st.translate("GGS"));
+ assertNull(st.translate("ATS"));
+
+ // K is T or G
+ assertEquals("S", st.translate("TCK"));
+ assertNull(st.translate("ATK"));
+
+ // M is C or A
+ assertEquals("T", st.translate("ACM"));
+ // Arginine first base variation
+ assertEquals("R", st.translate("MGA"));
+ assertEquals("R", st.translate("MGG"));
+ assertNull(st.translate("TAM"));
+
+ // D is A, G or T
+ assertEquals("P", st.translate("CCD"));
+ assertNull(st.translate("AAD"));
+
+ // V is A, C or G
+ assertEquals("V", st.translate("GTV"));
+ assertNull(st.translate("TTV"));
+
+ // H is A, C or T
+ assertEquals("A", st.translate("GCH"));
+ assertEquals("I", st.translate("ATH"));
+ assertNull(st.translate("AGH"));
+
+ // B is C, G or T
+ assertEquals("P", st.translate("CCB"));
+ assertNull(st.translate("TAB"));
+
+ // R is A or G
+ // additional tests for JAL-1685 (resolved)
+ assertEquals("L", st.translate("CTR"));
+ assertEquals("V", st.translate("GTR"));
+ assertEquals("S", st.translate("TCR"));
+ assertEquals("P", st.translate("CCR"));
+ assertEquals("T", st.translate("ACR"));
+ assertEquals("A", st.translate("GCR"));
+ assertEquals("R", st.translate("CGR"));
+ assertEquals("G", st.translate("GGR"));
+ assertEquals("R", st.translate("AGR"));
+ assertEquals("E", st.translate("GAR"));
+ assertEquals("K", st.translate("AAR"));
+ assertEquals("L", st.translate("TTR"));
+ assertEquals("Q", st.translate("CAR"));
+ assertEquals("*", st.translate("TAR"));
+ assertEquals("*", st.translate("TRA"));
+ // Arginine first and third base ambiguity
+ assertEquals("R", st.translate("MGR"));
+ assertNull(st.translate("ATR"));
+
+ // N is any base; 8 proteins accept any base in 3rd position
+ assertEquals("L", st.translate("CTN"));
+ assertEquals("V", st.translate("GTN"));
+ assertEquals("S", st.translate("TCN"));
+ assertEquals("P", st.translate("CCN"));
+ assertEquals("T", st.translate("ACN"));
+ assertEquals("A", st.translate("GCN"));
+ assertEquals("R", st.translate("CGN"));
+ assertEquals("G", st.translate("GGN"));
+ assertNull(st.translate("ATN"));
+ assertNull(st.translate("ANT"));
+ assertNull(st.translate("NAT"));
+ assertNull(st.translate("ANN"));
+ assertNull(st.translate("NNA"));
+ assertNull(st.translate("NNN"));
+
+ // some random stuff
+ assertNull(st.translate("YWB"));
+ assertNull(st.translate("VHD"));
+ assertNull(st.translate("WSK"));
+ }
+
+ /**
+ * Test a sample of codon translations involving ambiguity codes. Should
+ * return a protein value where the ambiguity does not affect the translation.
+ */
+ @Test(groups = { "Functional" })
+ public void testTranslate_nonStandardTableAmbiguityCodes()
+ {
+ GeneticCodeI standard = GeneticCodes.getInstance()
+ .getStandardCodeTable();
+
+ /*
+ * Vertebrate Mitochondrial (Table 2)
+ */
+ GeneticCodeI gc = GeneticCodes.getInstance().getCodeTable("2");
+ // AGR is AGA or AGG - R in standard code, * in table 2
+ assertEquals(gc.translate("AGR"), "*");
+ assertEquals(standard.translate("AGR"), "R");
+ // TGR is TGA or TGG - ambiguous in standard code, W in table 2
+ assertEquals(gc.translate("TGR"), "W");
+ assertNull(standard.translate("TGR"));
+
+ /*
+ * Yeast Mitochondrial (Table 3)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("3");
+ // CTN is L in standard code, T in table 3
+ assertEquals(gc.translate("ctn"), "T");
+ assertEquals(standard.translate("CTN"), "L");
+
+ /*
+ * Alternative Yeast Nuclear (Table 12)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("12");
+ // CTG is S; in the standard code CTN is L
+ assertEquals(gc.translate("CTG"), "S");
+ assertNull(gc.translate("CTK")); // K is G or T -> S or L
+ assertEquals(standard.translate("CTK"), "L");
+ assertEquals(gc.translate("CTH"), "L"); // H is anything other than G
+ assertEquals(standard.translate("CTH"), "L");
+ assertEquals(standard.translate("CTN"), "L");
+
+ /*
+ * Trematode Mitochondrial (Table 21)
+ */
+ gc = GeneticCodes.getInstance().getCodeTable("21");
+ // AAR is K in standard code, ambiguous in table 21 as AAA=N not K
+ assertNull(gc.translate("AAR"));
+ assertEquals(standard.translate("AAR"), "K");
+ }
+
+ @Test(groups = "Functional")
+ public void testTranslateCanonical()
+ {
+ GeneticCodes codes = GeneticCodes.getInstance();
+
+ GeneticCodeI gc = codes.getCodeTable("1");
+ assertNull(gc.translateCanonical("XYZ"));
+ assertEquals(gc.translateCanonical("AGA"), "R");
+ // translateCanonical should not resolve ambiguity codes
+ assertNull(gc.translateCanonical("TGY"));
+
+ gc = codes.getCodeTable("2");
+ assertNull(gc.translateCanonical("AGR"));
+ assertEquals(gc.translateCanonical("AGA"), "*"); // variant
+ assertEquals(gc.translateCanonical("ttc"), "F"); // non-variant
+ }
+}
"Failed command : -open examples/uniref50.fa" },
{ "CMD [-nosortbytree] executed successfully!",
"Failed command : -nosortbytree" },
- { "CMD [-dasserver nickname=www.test.com] executed successfully!",
- "Failed command : -dasserver nickname=www.test.com" },
{
"CMD [-features examples/testdata/plantfdx.features] executed successfully!",
"Failed command : -features examples/testdata/plantfdx.features" },
{ "CMD [-nousagestats] executed successfully!",
"Failed command : -nousagestats" },
{ "CMD [-noquestionnaire] executed successfully!",
- "Failed command : -noquestionnaire nickname=www.test.com" } };
+ "Failed command : -noquestionnaire" } };
}
import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureColourI;
+import jalview.api.FinderI;
import jalview.datamodel.Alignment;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
* seq1 feature in columns 4-6 is hidden
* seq2 feature in columns 6-7 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
af.getFeatureRenderer().setColour("Metal", fc);
/*
* test Match/Find works first
*/
- Finder f = new Finder(af.getViewport().getAlignment(), null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("M+");
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
assertFalse(hc.equals(hc2));
assertTrue(al.setHiddenColumns(hc)); // 'changed'
}
+
+ @Test(groups = { "Functional" })
+ public void testGetWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getWidth());
+
+ // width includes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(9, a.getWidth());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetVisibleWidth()
+ {
+ SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+ SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+ SequenceI seq3 = new Sequence("seq2", "-PQR");
+ AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+ assertEquals(9, a.getVisibleWidth());
+
+ // width excludes hidden columns
+ a.getHiddenColumns().hideColumns(2, 5);
+ assertEquals(5, a.getVisibleWidth());
+ }
}
import jalview.analysis.AlignmentGenerator;
import jalview.gui.JvOptionPane;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
import java.util.Arrays;
import java.util.BitSet;
assertEquals(sg.getStartRes(), 10);
assertEquals(sg.getEndRes(), 19);
}
+
+ @Test(groups = { "Functional" })
+ public void testFilterAnnotations()
+ {
+ ColumnSelection cs = new ColumnSelection();
+
+ /*
+ * filter with no conditions clears the selection
+ */
+ Annotation[] anns = new Annotation[] { null };
+ AnnotationFilterParameter filter = new AnnotationFilterParameter();
+ cs.addElement(3);
+ int added = cs.filterAnnotations(anns, filter);
+ assertEquals(0, added);
+ assertTrue(cs.isEmpty());
+
+ /*
+ * select on description (regex)
+ */
+ filter.setRegexString("w.rld");
+ filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
+ Annotation helix = new Annotation("(", "hello", '<', 2f);
+ Annotation sheet = new Annotation("(", "world", '<', 2f);
+ added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+ filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(2));
+
+ /*
+ * select on label (invalid regex, exact match)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setRegexString("(");
+ filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
+ added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+ filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select Helix (secondary structure symbol H)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setFilterAlphaHelix(true);
+ helix = new Annotation("x", "desc", 'H', 0f);
+ sheet = new Annotation("x", "desc", 'E', 1f);
+ Annotation turn = new Annotation("x", "desc", 'S', 2f);
+ Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 },
+ filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(1));
+
+ /*
+ * select Helix and Sheet (E)
+ */
+ filter.setFilterBetaSheet(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select Sheet and Turn (S)
+ */
+ filter.setFilterAlphaHelix(false);
+ filter.setFilterTurn(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(2));
+ assertTrue(cs.contains(3));
+
+ /*
+ * select value < 2f (ann1, ann2)
+ */
+ filter = new AnnotationFilterParameter();
+ filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+ filter.setThresholdValue(2f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(2));
+
+ /*
+ * select value > 2f (ann4 only)
+ */
+ filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(4));
+
+ /*
+ * select >2f or Helix
+ */
+ filter.setFilterAlphaHelix(true);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(2, added);
+ assertTrue(cs.contains(1));
+ assertTrue(cs.contains(4));
+
+ /*
+ * select < 1f or Helix; one annotation matches both
+ * return value should only count it once
+ */
+ filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+ filter.setThresholdValue(1f);
+ added = cs
+ .filterAnnotations(new Annotation[]
+ { null, helix, sheet, turn, ann4 }, filter);
+ assertEquals(1, added);
+ assertTrue(cs.contains(1));
+ }
}
assertEquals(5, m.getEnd());
}
+ @Test(groups = { "Functional" })
+ public void testMatchContains()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
+
+ assertTrue(m.contains(seq1, 2, 5));
+ assertTrue(m.contains(seq1, 3, 5));
+ assertTrue(m.contains(seq1, 2, 4));
+ assertTrue(m.contains(seq1, 3, 3));
+
+ assertFalse(m.contains(seq1, 2, 6));
+ assertFalse(m.contains(seq1, 1, 5));
+ assertFalse(m.contains(seq1, 1, 8));
+ assertFalse(m.contains(seq2, 3, 3));
+ assertFalse(m.contains(null, 3, 3));
+ }
+
/**
* test markColumns for creating column selections
*/
"Didn't set expected number of columns in total for two successive marks",
2, tbs.cardinality());
}
+
+ /**
+ * Test to verify adding doesn't create duplicate results
+ */
+ @Test(groups = { "Functional" })
+ public void testAddResult()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr = new SearchResults();
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getSize());
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getSize());
+ sr.addResult(seq1, 3, 6);
+ assertEquals(2, sr.getSize());
+ }
}
* seq1 feature in columns 1-5 is hidden
* seq2 feature in columns 6-10 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
alignFrame.getFeatureRenderer().setColour("Metal", fc);
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
+import jalview.schemes.FeatureColourTest;
import jalview.util.matcher.Condition;
import java.awt.Color;
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
});
seq.addSequenceFeature(sf);
}
+
+ /**
+ * @see FeatureColourTest#testGetDescription()
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testGetColorTooltip() throws IOException
+ {
+ assertNull(FeatureSettings.getColorTooltip(null, false));
+
+ /*
+ * simple colour
+ */
+ FeatureColourI fc = new FeatureColour(Color.black);
+ String simpleTooltip = "Click to edit, right-click for menu";
+ assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
+ assertNull(FeatureSettings.getColorTooltip(fc, false));
+
+ /*
+ * graduated colour tooltip includes description of colour
+ */
+ fc.setColourByLabel(true);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Label</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Label<br>" + simpleTooltip + "</br></html>");
+
+ /*
+ * graduated colour with threshold is html-encoded
+ */
+ fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
+ fc.setBelowThreshold(true);
+ fc.setThreshold(4f);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (< 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Score (< 4.0)<br>" + simpleTooltip
+ + "</br></html>");
+
+ fc.setAboveThreshold(true);
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (> 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
+ "<html>By Score (> 4.0)<br>" + simpleTooltip
+ + "</br></html>");
+ }
}
/*
* now threshold to Score > 1.1 - should exclude sf2
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
Color.white, 0f, 2f);
fc.setAboveThreshold(true);
fc.setThreshold(1.1f);
* now threshold to Score > 1.1 - should exclude sf2
* (and there should be no empty STARTGROUP/ENDGROUP output)
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
Color.white, 0f, 2f);
fc.setAboveThreshold(true);
fc.setThreshold(1.1f);
import java.awt.Color;
import java.util.Map;
-import junit.extensions.PA;
-
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class SequenceAnnotationReportTest
{
/*
* then with colour by an attribute the feature lacks
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10);
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+ null, 5, 10);
fc.setAttributeName("Pfam");
fr.setColour("METAL", fc);
sb.setLength(0);
FeatureRendererModel fr = new FeatureRenderer(null);
Map<String, float[][]> minmax = fr.getMinMax();
- FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22);
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
+ null, 12, 22);
fc.setAttributeName("clinical_significance");
fr.setColour("METAL", fc);
minmax.put("METAL", new float[][] { { 0f, 1f }, null });
// with showDbRefs = true, colour Variant features by clinical_significance
sb.setLength(0);
- FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3);
+ FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
+ null, 2, 3);
fc.setAttributeName("clinical_significance");
fr.setColour("Variant", fc);
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
*/
Color min = new Color(100, 50, 150);
Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fr.setColour("kd", fc);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
*/
Color min = new Color(100, 50, 150);
Color max = new Color(200, 0, 100);
- FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+ FeatureColourI fc = new FeatureColour(null, min, max, null, 0, 10);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
fr.setColour(kdFeature, fc);
* give "Type3" features a graduated colour scheme
* - first with no threshold
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red, null, 0f,
- 10f);
+ FeatureColourI gc = new FeatureColour(Color.green, Color.yellow,
+ Color.red, null, 0f, 10f);
fr.getFeatureColours().put("Type3", gc);
features = fr.findFeaturesAtColumn(seq, 8);
assertTrue(features.contains(sf4));
* graduated colour by score, no threshold, no score
*
*/
- FeatureColourI gc = new FeatureColour(Color.yellow, Color.red,
- Color.green, 1f, 11f);
+ FeatureColourI gc = new FeatureColour(Color.red, Color.yellow,
+ Color.red, Color.green, 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
assertEquals(fr.getColour(sf1), Color.green);
* threshold is min-max; now score 6 is 1/6 of the way from 5 to 11
* or from yellow(255, 255, 0) to red(255, 0, 0)
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 5f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 5f, 11f);
fr.getFeatureColours().put("Cath", gc);
gc.setAutoScaled(false); // this does little other than save a checkbox setting!
assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
* colour by feature attribute value
* first with no value held
*/
- gc = new FeatureColour(Color.yellow, Color.red, Color.green, 1f, 11f);
+ gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
+ 1f, 11f);
fr.getFeatureColours().put("Cath", gc);
gc.setAttributeName("AF");
assertEquals(fr.getColour(sf2), Color.green);
/*
* feature score outwith colour threshold (score > 2)
*/
- FeatureColourI fc = new FeatureColour(Color.white, Color.black,
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
Color.white, 0, 10);
fc.setAboveThreshold(true);
fc.setThreshold(2f);
Color result = testee.shadeCalculation(ann, col);
assertEquals(result, expected, "for column " + col);
}
+
+ /*
+ * test for boundary case threshold == graphMax (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMax;
+ Color result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ ann.threshold.value = thresh; // reset
}
/**
Color result = testee.shadeCalculation(ann, col);
assertEquals(result, expected, "for column " + col);
}
+
+ /*
+ * test for boundary case threshold == graphMin (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMin;
+ Color result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ ann.threshold.value = thresh; // reset
}
/**
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.schemes;
-
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class DnaCodonTests
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testAmbiguityCodeGeneration()
- {
- assertTrue(ResidueProperties.ambiguityCodes.size() > 0);
- }
-
- @Test(groups = { "Functional" })
- public void testAmbiguityCodon()
- {
- for (String ac : ResidueProperties.ambiguityCodes.keySet())
- {
- assertTrue("Couldn't resolve GGN as glycine codon",
- ResidueProperties.codonHash2.get("GG" + ac).equals("G"));
- }
- }
-
- @Test(groups = { "Functional" })
- public void regenerateCodonTable()
- {
- for (Map.Entry<String, String> codon : ResidueProperties.codonHash2
- .entrySet())
- {
- System.out.println("ResidueProperties.codonHash2.set(\""
- + codon.getKey() + "\", \"" + codon.getValue() + "\");");
- }
- }
-}
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import junit.extensions.PA;
-
public class FeatureColourTest
{
}
@Test(groups = { "Functional" })
+ public void testConstructors()
+ {
+ FeatureColourI fc = new FeatureColour();
+ assertNull(fc.getColour());
+ assertTrue(fc.isSimpleColour());
+ assertFalse(fc.isColourByLabel());
+ assertFalse(fc.isGraduatedColour());
+ assertFalse(fc.isColourByAttribute());
+ assertEquals(Color.white, fc.getMinColour());
+ assertEquals(Color.black, fc.getMaxColour());
+
+ fc = new FeatureColour(Color.RED);
+ assertEquals(Color.red, fc.getColour());
+ assertTrue(fc.isSimpleColour());
+ assertFalse(fc.isColourByLabel());
+ assertFalse(fc.isGraduatedColour());
+ assertFalse(fc.isColourByAttribute());
+ assertEquals(ColorUtils.bleachColour(Color.RED, 0.9f),
+ fc.getMinColour());
+ assertEquals(Color.RED, fc.getMaxColour());
+
+ }
+
+ @Test(groups = { "Functional" })
public void testCopyConstructor()
{
/*
/*
* min-max colour
*/
- fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+ fc = new FeatureColour(null, Color.gray, Color.black, Color.gray, 10f,
+ 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc1 = new FeatureColour(fc);
/*
* min-max-noValue colour
*/
- fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+ fc = new FeatureColour(Color.red, Color.gray, Color.black, Color.green,
+ 10f, 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc1 = new FeatureColour(fc);
assertTrue(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
+ assertFalse(fc1.isSimpleColour());
assertFalse(fc1.isColourByAttribute());
assertNull(fc1.getAttributeName());
assertTrue(fc1.isAboveThreshold());
assertEquals(Color.gray, fc1.getMinColour());
assertEquals(Color.black, fc1.getMaxColour());
assertEquals(Color.green, fc1.getNoColour());
+ assertEquals(Color.red, fc1.getColour());
assertEquals(10f, fc1.getMin());
assertEquals(20f, fc1.getMax());
/*
* colour by attribute (value)
*/
- fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+ fc = new FeatureColour(Color.yellow, Color.gray, Color.black,
+ Color.green, 10f, 20f);
fc.setAboveThreshold(true);
fc.setThreshold(12f);
fc.setAttributeName("AF");
assertTrue(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
assertTrue(fc1.isColourByAttribute());
+ assertFalse(fc1.isSimpleColour());
assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
assertTrue(fc1.isAboveThreshold());
assertEquals(12f, fc1.getThreshold());
assertEquals(Color.gray, fc1.getMinColour());
assertEquals(Color.black, fc1.getMaxColour());
assertEquals(Color.green, fc1.getNoColour());
+ assertEquals(Color.yellow, fc1.getColour());
assertEquals(10f, fc1.getMin());
assertEquals(20f, fc1.getMax());
}
@Test(groups = { "Functional" })
- public void testCopyConstructor_minMax()
- {
- /*
- * graduated colour
- */
- FeatureColour fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
- assertTrue(fc.isGraduatedColour());
- assertFalse(fc.isColourByLabel());
- assertFalse(fc.isColourByAttribute());
- assertNull(fc.getAttributeName());
- assertEquals(1f, fc.getMin());
- assertEquals(5f, fc.getMax());
-
- /*
- * update min-max bounds
- */
- FeatureColour fc1 = new FeatureColour(fc, 2f, 6f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(2f, fc1.getMin());
- assertEquals(6f, fc1.getMax());
- assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * update min-max bounds - high to low
- */
- fc1 = new FeatureColour(fc, 23f, 16f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(23f, fc1.getMin());
- assertEquals(16f, fc1.getMax());
- assertTrue((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * graduated colour by attribute
- */
- fc1.setAttributeName("AF");
- fc1 = new FeatureColour(fc1, 13f, 36f);
- assertTrue(fc1.isGraduatedColour());
- assertFalse(fc1.isColourByLabel());
- assertTrue(fc1.isColourByAttribute());
- assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
- assertEquals(13f, fc1.getMin());
- assertEquals(36f, fc1.getMax());
- assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
- /*
- * colour by label
- */
- fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
- fc.setColourByLabel(true);
- assertFalse(fc.isGraduatedColour());
- assertTrue(fc.isColourByLabel());
- assertFalse(fc.isColourByAttribute());
- assertNull(fc.getAttributeName());
- assertEquals(1f, fc.getMin());
- assertEquals(5f, fc.getMax());
-
- /*
- * update min-max bounds
- */
- fc1 = new FeatureColour(fc, 2f, 6f);
- assertFalse(fc1.isGraduatedColour());
- assertTrue(fc1.isColourByLabel());
- assertFalse(fc1.isColourByAttribute());
- assertNull(fc1.getAttributeName());
- assertEquals(2f, fc1.getMin());
- assertEquals(6f, fc1.getMax());
-
- /*
- * colour by attribute text
- */
- fc1.setAttributeName("AC");
- fc1 = new FeatureColour(fc1, 13f, 36f);
- assertFalse(fc1.isGraduatedColour());
- assertTrue(fc1.isColourByLabel());
- assertTrue(fc1.isColourByAttribute());
- assertArrayEquals(new String[] { "AC" }, fc1.getAttributeName());
- assertEquals(13f, fc1.getMin());
- assertEquals(36f, fc1.getMax());
- }
-
- @Test(groups = { "Functional" })
public void testGetColor_simpleColour()
{
FeatureColour fc = new FeatureColour(Color.RED);
* score 0 to 100
* gray(128, 128, 128) to red(255, 0, 0)
*/
- FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
+ FeatureColour fc = new FeatureColour(null, Color.GRAY, Color.RED, null,
+ 0f, 100f);
// feature score is 75 which is 3/4 of the way from GRAY to RED
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
null);
public void testGetColor_aboveBelowThreshold()
{
// gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
- FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
- 150f);
+ FeatureColour fc = new FeatureColour(null, Color.WHITE, Color.BLACK,
+ Color.white, 50f, 150f);
SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
null);
* graduated colour by score, no threshold
* - default constructor sets noValueColor = minColor
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
+ fc = new FeatureColour(null, Color.GREEN, Color.RED, Color.GREEN, 12f,
+ 25f);
String greenHex = Format.getHexString(Color.GREEN);
String expected = String.format(
"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
/*
* graduated colour by score, no threshold, no value gets min colour
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
+ fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.GREEN,
+ 12f, 25f);
expected = String.format(
"domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
redHex);
/*
* graduated colour by score, no threshold, no value gets max colour
*/
- fc = new FeatureColour(Color.GREEN, Color.RED, Color.RED, 12f, 25f);
+ fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.RED,
+ 12f, 25f);
expected = String.format(
"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
redHex);
* graduated colour based on attribute value for AF
* given a min-max range of 0-100
*/
- FeatureColour fc = new FeatureColour(new Color(50, 100, 150),
- new Color(150, 200, 250), Color.yellow, 0f, 100f);
+ FeatureColour fc = new FeatureColour(Color.white,
+ new Color(50, 100, 150), new Color(150, 200, 250), Color.yellow,
+ 0f, 100f);
String attName = "AF";
fc.setAttributeName(attName);
assertFalse(fc.isOutwithThreshold(null));
assertFalse(fc.isOutwithThreshold(sf));
- fc = new FeatureColour(Color.white, Color.black, Color.green, 0f, 10f);
+ fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
+ 10f);
assertFalse(fc.isOutwithThreshold(sf)); // no threshold
fc.setAboveThreshold(true);
sf.setValue("AC", "junk");
assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
}
+
+ /**
+ * Test description of feature colour suitable for a tooltip
+ */
+ @Test(groups = { "Functional" })
+ public void testGetDescription()
+ {
+ /*
+ * plain colour
+ */
+ FeatureColour fc = new FeatureColour(Color.RED);
+ assertEquals(
+ String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
+ Color.red.getGreen(), Color.red.getBlue()),
+ fc.getDescription());
+
+ /*
+ * colour by label (no threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ assertEquals("By Label", fc.getDescription());
+
+ /*
+ * colour by attribute text (no threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ fc.setAttributeName("CLIN_SIG");
+ assertEquals("By CLIN_SIG", fc.getDescription());
+
+ /*
+ * colour by label (above score threshold)
+ */
+ fc = new FeatureColour();
+ fc.setColourByLabel(true);
+ fc.setAutoScaled(false);
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ assertEquals("By Label (Score > 12.5)",
+ fc.getDescription());
+
+ /*
+ * colour by label (below score threshold)
+ */
+ fc.setBelowThreshold(true);
+ assertEquals("By Label (Score < 12.5)",
+ fc.getDescription());
+
+ /*
+ * colour by attributes text (below score threshold)
+ */
+ fc.setBelowThreshold(true);
+ fc.setAttributeName("CSQ", "Consequence");
+ assertEquals(
+ "By CSQ:Consequence (Score < 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by score, no threshold
+ */
+ fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
+ assertEquals("By Score", fc.getDescription());
+
+ /*
+ * graduated colour by score, below threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setBelowThreshold(true);
+ assertEquals("By Score (< 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by score, above threshold
+ */
+ fc.setThreshold(12.5f);
+ fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
+ assertEquals("By Score (> 12.5)",
+ fc.getDescription());
+
+ /*
+ * graduated colour by attribute, no threshold
+ */
+ fc.setAttributeName("CSQ", "AF");
+ fc.setAboveThreshold(false);
+ fc.setAutoScaled(false);
+ assertEquals("By CSQ:AF", fc.getDescription());
+
+ /*
+ * graduated colour by attribute, above threshold
+ */
+ fc.setAboveThreshold(true);
+ fc.setAutoScaled(false);
+ assertEquals("By CSQ:AF (> 12.5)",
+ fc.getDescription());
+ }
}
package jalview.util;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
}
-
- @Test(groups = { "Functional" })
- public void testIsDasCoordinateSystem()
- {
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
- assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
- "PDB", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("PDB", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
- new DBRefEntry("PDB", "v1", "a1")));
- // "pdb" is converted to upper-case in DBRefEntry constructor
- assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
- new DBRefEntry("pdb", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
- "pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
- "Uniprot", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
- "UNIPROT", "v1", "a1")));
- assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
- new DBRefEntry("pdb", "v1", "a1")));
-
- assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
- "EMBL", "v1", "a1")));
- assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
- "embl", "v1", "a1")));
- }
-
/**
* Test 'parsing' a DBRef - non PDB case
*/
<taskdef resource="net/sf/antcontrib/antcontrib.properties">
<classpath>
- <pathelement location="${basedir}/utils/ant-contrib-0.3.jar"/>
+ <pathelement location="${basedir}/utils/ant-contrib-1.0b3.jar"/>
+ </classpath>
+</taskdef>
+<taskdef resource="net/sf/antcontrib/antlib.xml">
+ <classpath>
+ <pathelement location="${basedir}/utils/ant-contrib-1.0b3.jar"/>
</classpath>
</taskdef>
-<taskdef resource="net/sf/antcontrib/antlib.xml"/>
<target name="checkLang" description="Reports missing entries in language bundles compared to Message.properties">
<!-- adapted from http://stackoverflow.com/questions/14381660/ant-task-to-compare-two-properties-files -->
git://source.jalview.org / jalview.git / commitdiff
